Pokemon XD: Gale of Darkness Walkthrough Part One

The following synopsis are courtesy of Pokemon Source Advance

Opening Scene:

When you start the game, first you must press New Game from the menu, and select your characters name. The default main character's name is Michael, or you can input your own original name. I will refer to him character as Michael if i ever refer to him as anything other than 'You'.
The game begins, and you see the captain of the Libra and his first mate sailing peacefully across the ocean. Then, cue battle music and helicopters attack! Not only copters, but also Shadow Lugia appears and swoops up the ship at the command of one of the pilots. The crew is dumped overboard as Lugia hoists the ship into the air with its psychic powers and flies away, as mysteriously as it appears, leaving the crew to soak.
Immediately after, you're thrust into your first battle. You control a level 50 Salamance (f) and are fighting a level 50 Metagross (n). You have Earthquake, Dragon Dance, Dragon Claw, and Brick Break. The first and last are super effective, so I recommend using two earthquakes to knock him out. The trainer will use sludge bomb no matter what you do on the first turn, but you should win pretty fast.

Find Jovi!

Quick runthrough: Grab PDA, fight CHOBIN, get snag machine, pokeballs
Wait, that was a battle sim! In reality, which you return to you only have a level 10 Eevee(m). Exit the room to the south ,and circle the room to the northwest to reach another room where you’ll receive a cut secne introducing Professor Krane and your mother, they've been working on a new way to purify Pokemon, the purification chamber! Your mother then asks you to go and find Jovi, your sister. Krane also tells you to go and pick up the PDA in your room.
Leave to the west and circle around again to get another cut scene with the news. They're mentioning the Libra has vanished outside of Gaeton Port, and that it's cargo was a large number of Pokemon! Pop out of the room and down the elevator. Enter the room to the south, then the one to the west from the two available, it's your room, with a PDA and 3 potions.
You already have an email, telling you Adon was playing hide and seek with Jovi earlier. Well, he's upstairs and he says that she's gone to Dr. Kaminko's manor, a big weird house southeast of the lab. Take the elevator to the ground floor (it's north) and exit to the south. Outside, head left to grab a chest with two antidotes, then exit by heading south. This brings up the map where you can now head to Kaminko’s house.
Kaminko’s house is very creepy, with statues of legendary Pokemon in the courtyard. As you approach the door, Chobin will approach you, and attack you, thinking you to be a burglar!

Kamiko Aide Chobin - 150p
-Sunkern(m) lv5

He's very easy, so tackle and bite will take care of him in short notice. Then, he notices you were a kid, and so not a burglar, and is Michael. Suddenly... Jovi comes out of the house, and asks if you got lost (y/n), but she says there's no way to hide the answer from her. Then she invites you in.
Inside, Chobin shows some of Dr Kaminko’s inventions, such as the unhealthy sandals. The door to the east is locked, so head west to talk to the professor. It will cut scene to Jovi asking you if you need help to find the way home. She and her Minun, Mini join you. So, you can leave. But, you get an email from Dr. Krane saying you need to get home quickly. Easy as pie, just leave and select the lab. There's a cut scene as you arrive, as Jovi explains how you got lost, and how she forgot she was playing hide and seek. Head inside the right building and Dr Krane is in the room to the left. Enter, and he will show you the snag machine. He will also offer to explain it you ,and asks if you'd be willing to test if for them. You'll have no choice but to say yes ,and he explains it in more depth, including shadow Pokemon. You now get your first glimpse of the snag machine, and really it looks a little silly. You also get a new PDA option, Shadow Monitor. Dr Krane says to go back to the sim room, where you started the game, and his assistant give you five Pokeballs. Hurray, that's the earliest of any pokemon game yet!

Cipher attacks!

BUT, as you’re about to leave, some men in white suits come and abduct the doctor, knocking out everyone in their way. You approach, and someone notices you, as they shove the doctor into the van.

Spy Naps - 165p
-Teddiursa (m) lv11+ SHADOW POKEMON

The doctor will tell you to throw a pokeball at it, and you catch your second Pokemon! The guy is aghast that you have a snag machine, and they quickly run off, Doctor in tow. Oh dear. One screen flash later, you're inside and Jovi is in tears. She says Dr Krane anticipated more shadow Pokemon, and it looks like he was right. Your mother, Lily says they must complete the purify chamber without him, because it's so close to finished. She heads upstairs to the lab, and find her just west of Dr Krane's lab, and she asks you to run an errand for her, in Gaeton Port, due south. You need to grab the Machine port, in the parts shop, next to Emil's house. For those of you who remember, that's where the Libra vanished!
As you leave, the professor's assistant tells you to keep the snag machine, and hands you Krane Memo's 1 and 2, documents on shadow Pokemon. They appear in your items, and are for reviewing how to use the snag machine (in case you forget that you just need to throw a pokeball). Leave to the south, and go to the port!

Enter Verich, stage left

At the port, Jovi leads the way to the parts sh...Er, some great big angry man named Zook. He threatens your sister, so you step up and have a battle to decide who's in the right. Conveniently, he has a shadow Zangoose. BAM, some strange one man, MR VERICH appears and stops your battle, with the help of his bodyguards red and blue.
Mystery Man Ardos(blue) with Alakazam vs. Thug Zook with Zangoose Ardos gets a one hit KO, yay for mysterious heroes! Zook runs off, and Jovi thanks him. I wouldn't, we just lost a shadow Pokemon!
As you head off, another cut scene erupts as Acri comes to see if Jovi's okay. You learn that MR Verich is mysterious and shows up occasionally by boat. Then she warns you to be careful, and head off. What a kind stater of the obvious. The parts shop is to the northwest side of town, with a big P besides its doorway. Inside, the assistant is in charge, but he has no idea what to do, because the owner is over at the strange doctors house. He does, however give you an item to evolve your Eevee! into whatever flavor of Eevee you'd like, how thoughtful. Now we have to find the shop owner.
But first, there are some battles to take care of! Sailor Boat is to the north on the dock, and if you say you don’t believe he won a singing contest he'll challenge you to a battle you for a prize!

Sailor Bost - 96p
-Marill (m) lv6
-Whimsur (m) lv6

Another easy fight, and he hands you TM45 (Attract) when you beat him. The next dock over has Perr, the part shop owner’s son, fixing the rotating bridges. After a brief cut scene, he asks you to come to the shop again, because he'll get you the part you need. When you do, you get the MACHINE PART.
Outside, you can now take the rotating bridges to access more of the town. The second bridge over leads north to a chest with 3 Pokeballs, and a lighthouse containing 1 potion, 1 Parlyz heal (floor 1), 1 Awakening (floor 3), and a trainer battle!

Bodybuilder Kilen - 144p
-Zubat (f) lv6
-Poocheyna(m) lv10+ SHADOW POKEMON

Poocheyna's easy to catch too, so go ahead and win. Kilen says he joined some organization to get that Pokemon, but doesn’t elaborate. Head back down to the bottom, and take the stairs because it's almost faster. Leave, and head back to town. Take the rotating bridge one more notch (to the east) and fight another trainer, who doesn’t just spring on you, how polite. say yes to battle.

Casual Guy Clye - 330p
-Taillow (f) lv6
-Ledian (f) lv10+ SHADOW POKEMON

Be careful, because Ledian's a little harder to catch, and you'll need to attack it. but don't knock it out! After the battle, Clye thinks you took his Pokemon, but supposes you couldn't have. Maybe he's a little blind.
Take the rotating bridge back to shore, and to the east. You'll be politely introduced to the Pokemon center where you can heal your Pokemon for free. how nice. But there's nothing interesting there. The Pokemart is to the north, where the owner is fresh new to his job. You can but the basics, minus of course, Pokeballs. The sailor on the bottom right will give you a free potion. Upstairs you learn a few tricks to play the game, but nothing exciting.
North again is the Krabby club, where only tough trainers can enter. So, you have to battle your way in.

Navigator Berk -120p
-Wingull (m) lv6
-Lotad (f) lv6

After the battle, you learn that there is no rule about trainers, and he was just bored. Oh well, easy exp. Inside, there's nothing exciting, but you find out MR VERICH is around. Behind the stage, including the stairs is nothing important, but the other stairs is the VIP lounge. There's a man there to see if your first Pokemon likes you, and VERICH's bodyguards blocking him off. Downstairs in the second basement is a chest with a super potion, hurrah! But that's everything here, so you can leave. Now we go back to the lab with the machine part.

Agate Ahoy

rriving back, you get memos 3, 4 and 5 from the professor's assistant. More shadow Pokemon information. Upstairs, exactly where you left her is your mother. She asks you if the shadow Teddiursa is ready to purify yet, but it wouldn't be quite ready. Tell her so, and she says the purification chamber will be ready when it is. Then, she sends you to Agate village to purify your Pokemon at the RELIC STONE until the purify chamber is ready. It's under the care of a man named EAGUN (Mimi’s grandfather from the first game). Your sister has run off, so time to head to Agate Village!
Agate hasn’t changed from the first game, which is good for continuity. The entrance has a chest with a pokeball. Right in front of you however, there’s an old man outside the Pokemart who will battle!

Fun Old Man Clerr- 224p
Oddish (m) lv7
Machop (f) lv7

The Pokemart has all the same things from the first game, including the cologne to purify Pokemon. Still no Pokeballs. The giant tree is actually Eagun’s house, inside which is his wife who knew you were coming, and explains how he just stepped out. But he steps in as soon as she says it. He says hello, and heads off to the relic stone, which he conveniently forgets to tell you how to get to. The house is empty otherwise, so time to head outside.
Around the back of the tree house to the left is a hidden ramp down to a chest with three potions. There’s also an old lady here who will battle.

Old lady Belish –224p
-Poochyna (m) lv7
-Nincada (m) lv7

She gives you TM09 (bullet seed) when you win. Head back up to the tree-house and across the bridge east, then north an old man will share one his Taillow’s berries with you. It’s a Leppa Berry. The house you just passed is the day care, but nobody’s there at the moment except the name rater, who lets you rename Pokemon. Outside, and farther east is a chest containing one ether. Great. Back one bridge, and find the Pokemon center. Heal if you'd like, and continue on.
Down the hill from the Pokemon center, turning south is another trainer, trying to escape. Suspicious. Let’s make sure he doesn’t!

Bodybuilder Dosk –
-Tyorogue (m) lv7
-Grimer (m) lv8
-Zubat (m) lv8

This is the first battle that should take more than two or three turns, but not too difficult due to his low attack. He says he was trying to look at the relic stone, but can’t so he got lost in frustration. So, head north, into the cave leading towards the relic stone. As soon as you enter, you see a line of people, You can only battle them in order, and they won't let you skip anybody. Here goes!
Cool Trainer Gorps – 240p
-Zigzagoon (m) lv8
-Numel (m) lv8

A few steps further is Super trainer Jols – 800p
-Snubbull (f) lv8
-Corpish (m) lv8
-Lotad (m) lv8

A few steps further again
Matron Ladi –256p
-Cacnea (f) lv8
-Slugma (f) lv8

Beside her is chests with 2 Burn heal. Then, next trainer is,
Fun Old Man Cron – 288p
-Horsea (m) lv9
-Abra (f) lv9
-Shroomish (m) lv9

He’ll hand you a cologne case when you win, which you can store colognes in to purify your Pokemon. You can buy them at the Pokemart here in town. But that's for later. Inside the next entrance, Eagun is waiting, but he says you should have all your Pokemon ready to purify, so he’ll battle you for some experience.

Myth Trainer Eagun – 1,200p
-Pikachu (m) lv12

He’s impressed you beat Pikachu, even though it's not too hard seeing as you should have six pokemon by now, and tells you to use the relic stone. So, go ahead and purify any Pokemon you’d like, but only one because when you do, he’ll take you to his house. He tells you that professor Krane used to study the relic stone, and the kidnapping is worrisome. However, someone else was there, Vander. He lives at mount battle, and claims to have seen mysterious figures out in the desert. He grabs your PDA number so he can get a hold of you.

Mt Battle

Now I’m sure you have more than one Pokemon ready, so back to the relic stone and purify any others you might have ready. Time to leave. To Mount Battle!
A cut scene as you arrive has bodyguard red greeting you, and talking of the ethics of Pokemon battling. The man outside says Vander is one of the area leaders and you’ll need to talk to the receptionist. Near the door, there’s a chest containing one full heal.
Inside, to the right, on the to benches are the move teacher (white) and the move deleter (black). You now have to battle your way up Mt Battle to meet Vander. See Mt battle for detailed descriptions of the trainers. You’ll need to only battle the first three.
When you reach Vander, he’s in area 3, teaching a new Mt Battle recruit. He asks you to train the new recruit. When you beat him, you’re taken out of Mt Battle, to the reception. Vander mentions that the Cipher facility has seen a little action recently, and it might be related to the kidnapping. Great, now we know what to do. As you leave, you get an email saying the Agate village sells Pokeballs now. Great, now we can catch some more shadow Pokemon!

Cipher Base and the Hexagon Brothers Five

When you reach the base, you see the van the professor was stuffed into sitting outside. Walk to the right for a cut scene introducing the colorful POWER RANGERS! Er, I mean Hexagon brothers. They seem to have forgotten to count to six. Oh well, that makes them easy pickins. If you try to enter the building, they tell you need to fight them first. So, talk to red…. And get ready for a fight. You’re going to battle all six of them, but you’ll probably want to heal between battles. You don’t need to fight all of them to enter, but they each have shadow Pokemon (although you can come back later to collect any you decide not to fight), so save and get ready...

Cipher Peon Resix – 680p
-Slugma (m) lv14
-Houndour (f) lv17+ SHADOW POKEMON

Houndour is a little tough compared to the Pokemon you’ve fought so far, so be prepared to use a few extra pokeballs.

Cipher Peon BluSix – 680p
-Horsea (m) lv11
-Goldeen (f) lv12
-Spheal (f) lv17+ SHADOW POKEMON

Cipher Peon BrowSix – 680p
-Hoothoot (m) lv14
-Baltoy (u) lv17+ SHADOW POKEMON

If you leave now, and return, you’ll find them trying desperately to count to six. They still fail.

Cipher Peon YelloSix – 680p
-Electrike (m) lv12
-Chinchou (f) lv11
-Mareep (m) lv17+ SHADOW POKEMON

Cipher Peon PurpSix – 680p
-Koffing (f) lv10
-Grimer (m) lv11
-Tentacool (f) lv10
-Gulpin (m) lv17+ SHADOW POKEMON

Cipher Peon GreSix – 680p
-Oddish (m) lv9
-Cacnea (f) lv9
-Shroomish (f) lv9
-Lotad (m) lv8
-Pineco (m) lv9
-Seedot (f) lv17+ SHADOW POKEMON

Finally, after beating all six you can go inside. The left door opens to a large room, in which is a chest containing three Pokeballs. And to the room to the right of that, is a super potion. Exit, and enter the other side of the building there’s a PC and a healing thing. Just beyond, a peon will drop from the ceiling at you…

Cipher Peon Corla – 560p
-Duskull (m) lv14
-Skitty (m) lv14

When you beat her she returns to whence she came. Straight is an elevator take it downstairs. You arrive at an intersection, head west and enter the room to the south…

Cipher R&D Tekot –750p
-Clamperl (m) lv13
-Corpish (f) lv14
-Zubat (m) lv15

But the elevator is locked in this room, so go back to the intersection and head east. There’ll be a battle in the hallway.

Cipher Peon Javion –
-Doduo (f) lv13
-Taillow (m) lv14

Now, continue down the hall, and turn east. There’s an elevator here, take it because you’ll need it later. What? You can’t pick it up? Well, take it down a floor then. Just as you leave the elevator, another peon stops you.

Cipher Peon Crink – 560p
-Snorunt (f) lv15
-Barboach (m) lv14

This is the focal point of the base. The right elevator takes you to a lab containing a healing machine guarded by a ninja who gets the drop on you.

Cipher Peon Digor –680p
-Abra (m) lv17
-Machop (m) lv16
-Feebas (m) lv16
-Makuhita (m) lv16

Further into the room is a chest containing one ether. Head back down, the left and up, into another lab room. It’s split in half, with a chest in the bottom half, containing 3 super potions, and a fight in the top half.

Cipher R&D Morbit – 800p
-Spoink (m) lv16
-Lotad (m) lv14
-Staryu (u) lv14

Now, head down from here, and turn right when the road splits. There;s a chest with an ether at the end of the hallway. Finally, head down the left side to the end (past the elevator for now), where there will be a lab with two scientists arguing, since they’re in a bad mood, you have to fight them both.

Cipher R&D Elrok – 850p
-Swablu (f) lv17
-Wyanut (m) lv16
-Corsola (m) lv15

Cipher R&D Coffy – 850p
-Dustox (m) lv14
-Wingull (f) lv17
-Pineco (f) lv16
-Quilfish (f) lv15

There’s an elevator outside the room, so get on it. There’s a ninja at the top, whom you haev to fight

Cipher Peon Meda – 640p
-Natu (m) lv16
-Nincada (m) lv14
-Wailmer (m) lv15

Down the hall it forks, so head right. There’s a ninja with a shadow pokemon. grab it!

Cipher Peon Cabol – 720p
-Carvanah (m) lv15+ SHADOW POKEMON
-Magnimite (u) lv15
-Psyduck (f) lv15
-Remoraid (m) lv16

But that’s all, so head back to the fork and go up, then left at the next fork. There’s a chest way at the end with another ether. Grab it. Go back to the last fork and head up, there’s a door, guarded by a ninja.

Cipher Peon Nopia –
-Jigglypuff (m) lv15
-Chimecho (m) lv17
-Dunsparce (m) lv16

Two guys are inside wanting to get out of Cipher. They notice you and one attacks.

Cipher R&D Klots – 800p
-Snubbull (f) lv16
-Kecleon (f) lv16
-Shroomish (f) lv15+ SHADOW POKEMON

They run away, leaving the ID card behind on the table. Grab it and ignore the guy who doesn’t attack you. There’s also a chest far to the right, with a great ball in it. Now you have the key, head through the one way door upwards, and head to the left. And follow the path south, down the previously locked elevator. There’s an empty room with stairs here. Up the stairs is Dr. Krane and his captor, who immediately attacks you.

Cipher Peon Naps (second time) – 720
-Murcrow (m) lv18
-Ryhorn (m) lv18
-Slackoth (m) lv18
-Bedlum (m) lv18

After he runs away, Krane joins you and makes you leave right away. You can, however, take long enough to grab the leaf stone in the nearby chest.
Head back outside, but wait! You’re stopped again by Lovrina, who wants the professor to help her. Refuse, and she attacks!

Cipher Admin Lovrina – 2000p
-Luvdisk (f) lv20
-Beautifly (m) lv19
-Roslia (m) lv19
-Delicatty (f) lv18+ SHADOW POKEMON

She’s a little hard, but she runs off when you win, so you can head all the way back to the lab without any more interruptions. If you come back here later, the Hexagon brothers are still counting, and you can fight them again.

Pyrite and ONBS

Back at the lab now, you get a cutscene saying the purify chamber was completed while you were rescuing the professor, but they thank you for rescuing him anyways.
The purify chamber works like this: There are nine sets to the purify chamber, one shadow Pokemon (aka visitor) can be placed in the center of each set, so nine shadow Pokemon total. Four regular Pokemon can be placed in each set around the shadow Pokemon visitor. These regular Pokemon alter how fast the purification will take.
The speed the Pokemon is purified is referred to as the flow, the flow can be increased by increasing the tempo. The direction the shadow Pokemon faces is important, as to get the highest flow, they should be facing a Pokemon they are super effective against, so you need to know your types too!
The tempo of the set is determined by the non-shadow Pokemon involved. More regular Pokemon, mean higher tempo, flow and less time to purify! But remember your types, you’ll need type matchups in a circle following the flow (clockwise).
The chamber works more the longer you leave the Pokemon in it, and you can access it from the PC, useful! Even more useful is that you can head straight to the lab and the Pokemon is all the way purified, no more stops at the relic stone if you don’t feel like it.
When you leave, Krane asks on the progress of the rom, lily says it will be ready soon. Your mother asks you to check up on Datan for it, and he’s next to the directors office. Jovi runs off, probably to do what you were just asked, so you’ve got to chase her first. When you catch up, she says she can’t find him. Asking around, you find that he’s upset about something, and went downstairs and outside. Datan is hiding to the right just before you leave the map, and he’s distressed because the rom is so heavily encrypted that he can’t break it. Krane then arrives, and has an idea of who can help. His name is Nett and he works for Onbs in Pyrite town (remember from the first game). You’re handed the rom and told that Onbs is actually a TV station who helped with Cipher last time. He’s Secc’s right hand man, and is the only man who can do that job.

Pyrite Town

So, you head off, and arrive in pyrite town. When you do, you find a cameraman running to find Marcia. Who could they be? Cail at the gate says Marcia’s always running off like that. Then, he asks if you’d like to battle!

Rogue Cail – (?)
-Ralts (f) lv16
-Snubbull (m) lv16
-Seedot (m) lv16
-Houndour (f) lv16

He’s easy if you’ve fought everyone so far. After the fight he ignores you… ah well. The jail, the first one on the right, there’s a chest with a hyper potion in the room immediately to the right of the entrance. A little while farther, a cut scene shows TRUDLY and FOLLY getting singled out by a cop, and running off. A little further is the next shop, with again nothing special. Just beyond, a man in an orange hat offers you a battle.

Worker Dobbit – 320p
-Spoink (m) lv16
-Magnemite (u) lv16
-Numel (m) lv16

Up ahead, the great big orange building is the hotel, which acts as a Pokemon center, but you have to pay 100p. But you can still raid it. The leftmost room of the circular interior has a chest with a Parlyz heal. The northeast has a chest with a focus band, and the rightmost has 3 Great balls! Hurrah, for those hard to catch Pokemon.
Outside again is a circle on the ground, with five trainers standing around it. None will give you the option to avoid the battle for a moment, and they will battle you over and over again, as long as you ask. For now it’s a great way to gain some exp. So, let’s save and get moving. Starting at the bottom, and working counter clockwise (to the right), we have:

Chaser Finol – 340p
-Shuppet (f) lv16
-Ledian (f) lv16
-Remoraid (m) lv16
-Togepi (f) lv17

Raider Dert – 160p
-Slugma (f) lv16
-Natu (f) lv16
-Oddish (f) lv16

Bodybuilder Doby – 408p
-Machop (m) lv17
-Tentacool (m) lv17

Chaser Labet – 340p
-Swinub (f) lv17
-Bagon (f) lv17
-Murkrow (m) lv17
-Clamperl (f) lv17

Hunter Raling – 272p
-Zigzagoon (f) lv17
-Whimsur (m) lv17
-Aipom (m) lv17
-Dunsparce (f) lv17

Once you’re done with this lot, head to the great big white building. There’s a vending machine beside the door, so grab some good cheap healing items if you’d like. Then, head inside.
Upwards from the door and down the only hall to the right are a few rooms and an elevator, take it. Upstairs, you walk straight down, into Secc’s room, where he manages ONBS with Nett. Nett’s not in the room, at the moment, but Secc tells you to go find him. So, follow the hallway south, past the mysterious locked door. There’s a girl in the back of the first room, who asks you to find her mom, say yes and she’ll follow you around. The next room you enter is the news room, where they’re filming a report about you rescuing Professor Krane. But, Nett’s not there, so back to the fork and hand a left. Time to go up another floor. The first door is a dressing room, with a chest in it. But you can’t reach it yet, so just walk past the room entirely. The room afterwards is another dressing room, where the reporter has lost her daughter. Find any young girls lately? Of course you have. Exit the room, and head up the stairs, because all that’s down the hall is another blocked chest.
On the roof, some guy doesn’t want you to disturb Nett, but Nett overhears and calls you inside. Here you meet Nett and Bitt, his assistant. He looks at the rom, and says it will take some time. He tells you to go and visit Duking, the mayor, out searching for wild Pokemon at a Poke-Spot. He grabs your number as you leave, so he can call you when he’s done.
When you leave the building, you find FOLLY and TRUDLY plotting something for a ‘boss’, which is rather disrespectful of ex-cipher-members. They then run off, leaving you to ponder the message they receive “come here right now”.
Past where they were, there’s a bridge, across it and to the right is a chest with a great ball. Make sure not to go close to Rokt, who’s running and will push you out of the way. Just circle around to the far top or bottom. Beyond him is the large spherical colleseum. You can't enter it with shadow pokemon, so you can leave it for later. Or, look it up in the colleseum section if you insist.

Poke Spot Adventure

Now, to the poke-spot, to find those wild Pokemon! You arrive as they’re shooting a news report with Duking talking about the poke-spot. He asks you to come and catch wild Pokemon for the viewers. He says you need Duking Brand Poke-Snacks to catch Pokemon (he hands you twn), then you must place any number of snacks on the poke-spot, and any Pokemon arriving will snack for a proportional length of time. A handy spot monitor (which Duking hands you) will let you keep track of your snacks, because wild Pokemon won’t appear while you’re around, only when you leave. This makes it a rather complicated system, but a great idea. He also gives you location of one of the other two poke-spots, where he’ll meet you when you arrive.
Duking then asks you a favor, like everyone else in the game. He asks you to catch Trapinch, Surskit, and Wooper who are rare Pokemon who hardly ever show up at Poke-spots. But not without reward, catch them and he’ll give you one of his Pokemon in exchange! He also gives you the location of the last poke-spot to thank you for agreeing to help him. It’s in a cave, so lets go check it out, but save first because as soon as you arrive you fight a shadow pokemon.
Oh dear, Folly and Trudly are there already, and talking about Miror B (the music man from the first game) who they work for. He arrives moments after you do, and he asks you to join him, because he can smell your Pokemon. Weird guy, just say no. He’ll say he already knew you’d be an enemy, so he attacks you of course! If you said Yes, he'll attack you anyways, because he assumes you must be lying. Phooey.

Wanderer Miror B – 440p
-Lombre (m) lv17
-Lombre (m) lv17
-Lombre (f) lv17
-Voltorb (u) lv19+ SHADOW POKEMON

After the fight, he threatens you and immediately runs off. But, he drops a Miror Radar, letting you know whenever Miror B (The boss) gets close. Nett then emails you saying he’s done with the Data Rom, and to chat with him back in Pyrite.

Trouble at the TV station

Oh no! when you arrive, the burly guard says there has been trouble, some shady characters showed up and took Megg hostage. Running up to the elevator, a ninja peon drops from the ceiling and attacks!

Cipher Peon Rett – 720p
-Carvanah (m) lv18
-Barbaroach (f) lv17

I’m really curious why they just sit on the ceiling. Maybe it’s training? Well, whatever, he returns to whatever he was doing, and you can pass by. Continue to the first door, and unlock the inner door. You rescue two people, and they tell you Megg is Nett’s little sister. The next room after that, there’s another peon hassling people, he notices you, so battle!

Cipher Peon Mocor – 720p
-Corpish (f) lv17
-Electrike (m) lv17
-Grimer (f) lv18

He vanishes, and you can go up the elevator, but save first because another shadow Pokemon approaches. Another ninja appears on the elevator when you exit, somehow. Where do these people keep coming from? He attacks you, after surprising your character.

Cipher Peon Torkin – 840p
-Kecleon (m) lv19
-Surskit (f) lv21
-Makuhita (m) lv18+ SHADOW POKEMON

How do they vanish too, I never understood how. But I suppose that’s why they wear the ninja outfits. The room immediately south of you has another peon, who of course attacks.

Cipher Peon Elox – 800p
-Doduo (f) lv20
-Tentacool (f) lv18
-Chimecho (m) lv20

You learn from Secc that they arrived for Nett, because of the data rom. Wow, what a surprise. South along the hallway, the room that was locked before contains 1 ether. Further along the hall is the news room where a peon is hassling the news lady for an autograph. Attack!

Cipher Peon Rixor – 800p
-Quilfish (f) lv19
-Ryhorn (m) lv20
-Chinchou (f) lv20
-Koffing (f) lv20

You’ve cleared him out of there, so time to head upstairs. But right before the elevator, another ninja!

Cipher Peon Mesin – 840p
-Spinarak (m) lv20
-Beautifly (f) lv19
-Dustox (m) lv20
-Vulpix (f) lv18+ SHADOW POKEMON

So, head upstairs and heal (hurrah). The first room has a revive, and the second has another peon, who attacks you.

Cipher Peon Dilly – 840
-Gulpin (f) lv19
-Mareep (f) lv18
-Luvdisk (m) lv20
-Bellossom (m) lv21

Before going up the stairs, head down the hall to the south to where a peon is in the prop room.

Cipher Peon Edlos – 840p
-Furret (f) lv19
-Zigzagoon (f) lv20
-Togetic (m) lv19
-Delibird (f) lv21

Inside the room is also an HP up, which is great for one of your Pokemon. Head upstairs now, BUT right before the stairs is another ninja. Tired of them yet? Well, fortunately this is the last ceiling space they could hide on.

Cipher Peon Lobar – 880p
-Sneasel (m) lv20
-Yanma (f) lv19
-Misdreavus (m) lv20
-Duskull (m) lv19+ SHADOW POKEMON

Now you can head upstairs to the room where Nett is. On the roof, the man who was guarding the door before notices you. So does the cipher peon he was fighting. Who, then attacks you.

Cipher Peon Feldas -920p
-Kadabra (m) lv22
-Flaffy (f) lv22
-Vigoroth (m) lv21
-Ralts (f) lv 20+ SHADOW POKEMON

The guard says they took the kidnapped Megg into Nett's room. When you enter, the peon complains how it's Nett, of all people who ended up with the disk. Nett hands over the data rom in order to keep the peon from harming his sister. The peon's are smarter than expected, they knew he'd make a copy and wiped the entire network of the TV station, too. He then lets Megg go, as you enter the room. But the cipher man turns and sees you, and attacks!

Cipher Cmdr Exol - ??
-Loudred (m) lv23
-Girafarig (f) lv23
-Mawhile (f) lv22+ SHADOW POKEMON
-Raichu (f) lv23

This guy's Girafarig constantly uses stomp, which is extremely strong so take it out first, and fast. Remeber that it's dark/normal, so it's immune to ghost and psychic. But, that also makes it double weak to fighting moves, so i reccomend taking Makuhita into this battle.
He says he doesnt need to stick around once he's got the data rom, so he runs off, clutching his prize. Nett then explains that Cipher's plans have become clear, and are clearly criminal. They were behind the attack on the Libra and are planning an attack on Phenac City. One of ONBS's star reporters has gone off to Phenac, and you have to run off to warn her and the mayor of the upcoming attack.

How to steal a city, Phenac Style

So, now you can leave, as all the Cipher fellows have left, if you didn't fight any already you can't now. If that means you missed a shadow pokemon Either Miror B will have it, or that same peon will appear later. Now, head out of the city, and towards Phenac.

Realgam Tower

In Phenac, a girl stops you and tells you you’re the one millionth Visitor and hands you a CD case and three Battle CDs. CD01, CD07, CD20. She tells you to go to Realgam tower to use them.
Quite frankly, there are no events here in Realgam tower. It contains three things you'll want to use when you're tired of story mode, a Colleseum, Battle Bingo, and the Battle Sims. When you arrive, you also run into Trudly and Folly who themselves grabbed a stack of battle CDs (for battle sims) but are discourages because they can't actually catch the pokemon on them, being holograms. They say they're going to throw their CDs out somewhere, which means you'll have a stack of them to find over the rest of the game.
If you run to the right at the entrance, there's a chest containing a protein, and inside (twice) is a Pokemon Center and a poke-mart. The Mart sells all sorts of TMs, so you can customize your pokemon. Inside one more is the atrium, with the colleseum (not yet in service) the Battle bingo to the left and the Battle sims to the right. But nothing exciting yet.

The Justy Six

Once you return to Phenac from Realgam tower, you're going to find the entire town deserted, including the Pokemart and Pokemon Center. To the right there’s a chest with three ultra balls behind the First house, and a music CD inside the second house of the right. There’s Also a bed here, where you can heal if you need to. The house on the top Left is the mayor’s, and right below it is a chest with 3 Hyper potions. You have to give the girl inside the Mayor's house the CD to get upstairs.
Beside the bed upstairs, on the left side is a note, from the mayor Saying that he’s noticed Cipher taking over key positions in the town. He asks Justy from the PPC (pre-gym) for help. However, the note ends abruptly just as the housesitter comes up behind you and transforms into a Cipher Ninja!

Cipher Peon Exinn – 920p
-Seviper (f) lv20
-Snorunt (f) lv20+ SHADOW POKEMON
-Golbat (m) lv21
-Mightyena (m) lv21

You’d better get out of here, but save first, as another ninja awaits Just downstairs.

Cipher Peon Gonrag –880p
-Murkrow (m) lv22
-Pineco (m) lv20+ SHADOW POKEMON
-Ariados (f) lv22

He leaves, and so can you. But when you leave, the Justy team appears, and THEY can count to six. Hmm, sound familiar? They all want to be admins, so they divide and conquer. Time to hunt and destroy. But not just the Justy's, members of the city are Cipher peons too! Gotta beat 'em all!
The woman in front of the gate, who gave you the CD case is a Ninja, when you talk to her next (but not a justy)!
Cipher Peon Pellim - 840p
-Sudowoodo (m) lv20
-Clamperl (m) lv21

So is the man in front of the item shop!
Cipher Peon Kapen - 880p
-Volbeat (m) lv20
-Spoink (m) lv21
-Illumise (f) lv20
-Seviper (m) lv21
-Wailmer (f) lv21

Once you beat him, you can get into the shop, that sells ultra balls! And immediately out side the Pokemon center is another Cipher.
Cipher Peon Fenton - 840p
-Goldeen (m) lv20
-Carvanah (f) lv20
-Koffing (f) lv21
-Mightiena (m) lv21

The man running around the fountain is a cipher too
Cipher Peon Forgs - 840p
-Duskull (f) lv21
-Corpish (f) lv20
-Quilfish (m) lv21

The gal outside where you got the music CD is a cipher
Cipher Peon Ertlig - 880p
-Poocheyna (m) lv22
-Magnemite (u) lv21
-Staryu (u) lv21
-Absol (m) lv21

Seriously, who names their kid Ertlig? Behind the music CD house is, guess!
Cipher Peon Ezoor - 840p
-Shuppet (m) lv21
-Teddiursa (f) lv21
-Corsola (m) lv21

I take it back, Ezoor's a weirder name. Now, that's all for the regular ciphers, lets head after the Justy's now. In front of the school
Cipher Peon Purpsix (2nd time) - 800p
-Koffing (f) lv20
-Grimer (m) lv20
-Tentacool (f) lv20
-Zubat (f) lv20
He leaves you Battle CD08 Outside where you got the music CD is another justy
Cipher Peon Resix (2nd time) - 800p
-Slugma (m) lv20
-Numel (f) lv20
He leaves Battle CD19 In front of the Mayors house
Cipher Peon Gresix (2nd time) - 800p
-Oddish (m) lv18
-Cacnea (f) lv18
-Shroomish (f) lv19
-Lotad (f) lv19
-Pineco (m) lv20
He leaves Battle CD28 Inside the Mayor's house are two Justys. They will attack you in order.
Cipher Peon Yellosix - 800p
-Electrike (m) lv20
-Chinchou (f) lv20
-Magnemite (u) lv20
He leaves Battle CD27
Cipher Peon Browsix - 800p
-Noctowl (m) lv20
-Vigoroth (m) lv20
He leaves Battle CD32 Left of town entrance
Cipher Peon Blusix - 800p
-Horsea (m) lv20
-Goldeen (f) lv20
-Beldum (u) lv19
He leaves Battle CD16

Once you've beaten all six, head to the PPC (school) in the center of town.
Save before you enter the pregym, because inside the Pregym, the every person you see is a ninja in disguise, with a shadow pokemon!
Cipher Peon Eloin – 1000p
-Kirila (m) lv22
-Linoon (f) lv20
-Natu (m) lv22+ SHADOW POKEMON

Up the stairs, right ahead, another Ninja, and another shadow pokemon!
Cipher Peon Fasin – 1000p
-Remoraid (m) lv22
-Golbat (m) lv22
-Roselia (f) lv22+ SHADOW POKEMON

This must be the real Justy, right? Nope! Another Ninja! He says that the real Justy and the Mayor are prisoners in the pre-gym's basement. Perfect!

Cipher Peon Fostin -880p
-Kadabra (m) lv22
-Sneasel (f) lv22
-Misdreavus (f) lv22
-Meowth (f) lv22+ SHADOW POKEMON

This guy keeps using double team, so either be fast, or buy some X accuracy, or you're going to start missing and might take some serious damage.
I guess we need to go to the basement now, but to get there we need an elevator key. He doesn't however tell us where it is before he runs off.

Phenac Colleseum

You can, however, follow the peon to the colleseum where you're stopped by that old guy again, who is (do i really need to tell you?) a ninja!

Cipher Peon Greck- 920p
-Torkoal (f) lv22
-Nuzleaf (m) lv23
-Swinub (m) lv22+ SHADOW POKEMON

Now you can get into the colleseum. Which is big and empty. shoot. both side doors lead to the same room, but save before you enter. Two ciphers lie in wait, and one attacks you.

Cipher Peon Ezin - 1000p
-Pelliper (m) lv23
-Electrike (f) lv23
-Spearow (m) lv22+ SHADOW POKEMON

then the other,
Cipher Peon Faltly - 1040p
-Chimecho (m) lv23
-Stantler (m) lv23
-Grimer (f) lv23+ SHADOW POKEMON

Now save. In the center of the huge room, a cinematic unfolds. Marcia, the TV reporter has a Cipher Admin sort of fellow cornered in the middle of the room who says he's been offered the position of govenor, but his political record would be smudged with the contents of the video tape Marcia took. She refuses to give the tape to him. He begins to threaten her, but notices you. MR. SNATTLE then reveals his name and tells his super-peon to get rid of you.

Cipher Peon Egrog - 1080p
-Hoothoot (m) lv25
-Graveler (m) lv26
-Gulpin (f) lv26
-Seel (f) lv23+ SHADOW POKEMON

The cameraman just missed your battle, because he's so freaked out. Marcia chides him, but Snattle says Master Greevil would be anoyed with pointless arguements. He then attacks you.

Cipher Admin Snattle - 2800p
-Lanturn (f) lv26
-Quagsire (m) lv26
-Lunatone (u) lv25+ SHADOW POKEMON
-Castform (f) lv27
-Metang (u) lv28

When you've cleaned him out, he's shocked. Gorigan, however, is finished whatever he was doing by now, so it doesnt matter. He decides to leave, but he vows to return. Marcia thanks you for saving her, and says that this time they DID manage to tape your battle. She's running back to pyrite to get it on the air. Then, they run off. Wait, what's that?
The elevator key! Great, lets go free the mayor, and the entire town. Boy, Cipher sure is thurogh. So, back to the pre-gym, and use the key on the right desk to open an elevator. Head down, and the whole town greets you, especially the mayor. He's astonished you're there, but when you explain what's happening, he thanks you heartily and everyone heads out. The mayor then tells you to visit him in his home later.
Justy then chips in and grabs your PDA number, in case he wants to help later. He says pheanac was attacked because of some rumors around of people heading into the desert. That puts a new spot on your map. As you try to leave, an old lady stops you to say thank you. Her grand daughter runs the day-care in Agate, so we can use it now! Yay!
It's funny how each person was exactly replaced by a cipher member. Anyways, back in the basement is Battle CD35 to the right, and a guy saying he lost his trapinch during the whole situation.
When you go talk to the mayor, he's in his house, at his desk. He says that as a token of appreciation from the town he's giving you the EXP. Share.

A new Cipher base?

When you try to head to the new base, the scooter gets stuck in the sand. deary me. So, you return to Phenac. You're greeted by the sympathetic woman at the gate, who says that No scooter could get through it. Then you get an email from Nett. He wants you to find a pokemon that was on the SS Libra, that ship that vanished at the beginning of the game. You have to visit him in Pyrite town.
So, we head all the way up that building. Why doesn't he move to the floor? Enter his house and Bitt greets you, saying he's astonished at what his reporter saw of you figting Cipher. He wants you to help an old man and his granddaughter. They want you to find their pokemon, Bonsly. The grandfather says his granddaughters pokemon was aboard, and that it was a new species of pokemon. He wants you to search for it. The girl has a photo if you need to know what it looks like. Bitt and Nett say it'll be hard to find it, but they'll try to help. They then notice you're covered in sand. So, you explain. Nett says it's probably Cipher's big hideout, and it won't be easy to investigate. Bitt says that maybe Perr in Gaeton port could lend a hand with something like that. That's the guy who gave us the machine part.

Continue onto Walkthrough Part Two

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