Realgam Tower: The general appearance of this place is still the same. But those rooms you used to fight the Cipher admins were replaced by marts and Pokémoncenters, and the only place to visit really is the central lobby. The left room will feature the game Battle de Bingo while the right the Battle Disc, and the central elevator, leading to the Realgam Colosseum, is under maintenance at the moment. Head back to Phenac.

Phenac City:
Now that the lady lets you in, you’ll will find the citizens appearing peculiar. The guy who used to have a Castform running after him now has a Duskull, while the trainer with a Marill now has a Mightyena. Head up the stairs to the mayor’s house, but his secretary says he’s out. Go to the house to the right side. And old man inside will give you a music CD on his table, saying that it isn’t his taste. He will also let you rest at his beds because the PokémonCenter in the city is for some reason out of order at the moment.

Head back to the mayor’s house, the secretary will want the music CD from you. She plays it and gets distracted, while you go up to explore the mayor’s room. You find a letter he wrote to Justy, the leader at Phenac’s training school, asking for help to fend off Cipher. But then the mayor’s secretary comes back up and reveals herself to be a Cipher peon. Fight her:

Cipher Peon Exinn - Snorunt 20+, Seviper 20, Golbat 22, Mightyena 21

Go downstaris, and another peon will fight you:

Cipher Peon Gonrag - Pineco 20+, Murkrow 22, Ariados 22

Now, head to the training school to deliver the letter, but to your horror, 6 Justys appear and scatter around in the city. Fight them all and you’ll discover that they’re the coloured peon brothers again:

Cipher Peon Jirel - Horsea 20, Goldeen 20, Beldum 19 - Battle Disc 16
Cipher Peon Resix - Slugma 20, Numel 20 - Battel Disc 19
Cipher Peon Purpsix - Grimer 20, Koffing 20, Tentacool 20, Zubat 20 - Battle Disc 08
Cipher Peon Greesix - Cacnea 18, Oddish 18, Shroomish 19, Lotad 19, Pineco 20 - Battle Disc 28

The last two you have to fight at the mayor’s house,
Cipher Peon Yellosix - Chinchou 20, Electrike 20, Magnemite 20
Cipher Peon Browsix - Noctowl 20, Vigoroth 20

You then go talk to everyone you see in the city, and they’ll all reveal themselves to be Cipher peons:

Cipher Peon Trita - Shuppet 21, Teddiursa 21, Corsola 21
Cipher Peon Kubara - Magnemite 21, Poochyena 22, Staryu 21, Absol 21
Cipher Peon Kuroru - Spoink 21, Volbeat 20, Illumise 20, Seviper 21, Wailmer 22
Cipher Peon Zanyu - Goldeen 21, Carvanha 21, Koffing 21, Mightyena 21
Cipher Peon Yaida - Duskull 21, Corphish 20, Qwilfish 21
Cipher Peon Rikoza - Sudowoodo 20, Clamperl 21
Cipher Peon Eloin - Linoone 22, Kirlia 20, Natu 22+
Cipher Peon Fasin - Golbat 22, Remoraid 22, Roselia 22+
Cipher Peon Fostin - Sneasel 22, Alakazam 22, Misdreavus 22, Meowth 22+

Some of these last ones you have to fight inside the training school. They will tell you about the real citizens being locked underground, then flee. Afterwards, fight the last peon guarding the entrace to the Phenac Stadium:

Cipher Peon Greck - Torkoal 22, Nuzleaf 23, Swinub 22+

Now, enter the stadium, and you will fight two more peons:

Cipher Peon Ezin - Pelipper 23, Electrike 23, Spearow 22+
Cipher Peon Faltly - Stantler 23, Chimecho 23, Grimer 23+

Then, standing in the middle of the staidum, you will see another Cipher Admin Snattle reasoning with Duking’s reporter daughter Leila, who refuses to hand over her recordings of Cipher’s evil acts in Phenac. He will fight you after his peon:

Cipher Peon Egrog - Graveller 26, Hoothoot 25, Gulpin 26, Seel 23+
Cipher Admin Snattle - Lanturn 26, Quagsire 26, Lunatone 25+, Castform 27, Metang 28

He storms away after dropping the elevator key, and you back to the training school to save everyone underground. The mayor Dagude thanks you, and gives you the experience share if you visit him at his house again. You also free the Agate daycare center people who happen to be visiting Phenac, which means you can now use the center in Agate. Like in Colosseum, it only admits one Pokémon a time, so no breeding.

Before you leave, Justy will tell you of a peculiar sighting to the north of Phenac, and a new location will unlock on your map. However, when you try going there, your scooter gets jammed by the sand everytime and you had to backtrack. Go back to Phenac, and you will receive another mail from Nett to go back to Pyrite.

Pyrite Town:
Back at the ONBS station, you will see a young girl an her grandpa searching for a Bonsly who should be riding on the cruiser Libra. She wants you to find it for her, and Nett suggests you head to the Gateon Port to seek help from Roose, the old man who used to sell stuff at the Under City 5 years ago before everyone moved above ground. Go there you will.

Gateon Port:
Head to the machinery shop again, and Zak, who’s actually Roose’s grandson, will tell you that his grandfather is working with Prof. Kaminko on some mecha Pokémon. Go to Kaminko’s House now.

Kaminko’s House:
You get stopped by Chobin again when you try to enter, who mistakes you as a thief yet again. Fight him:

Researcher Chobin - Sunkern 25, Gyarados 26

Prof. Kaminko will then appear to ask what is going on. Chobin says you are a thief, but then recognizes you. Kaminko wants to show off his newest and greatest inventions, and tells Chobin to retrieve it. Then, the Groudon statue in the fountain goes down while the water dries up, and Chobin reappears riding on a Robo Groudon. He fights you again:

Robo Groudon - Sunflora 26, Gyarados 26, Hoppip 26, Tropius 26

Defeat him, and the Robo Groudon will overload. Kaminko loses his interest in mecha Pokémon, but Chobin is determined to improve it. You head in and Kaminko will allow you to go into his secret room this time. Head down, and you will find Roose working on a Robo Kyogre. You tell you your situation, and he will take you back to Gateon Port and upgrade your scooter to the hover type. You are ready to explore the unaccessible site now. Before you leave, you will see Verich and his bodyguards sailing off on their cruiser.

Deserted Cruiser Libra:
You’ll see that it is the deserted cruiser Libra when you arrive, and you head in. This is the place where they have all these big boxes you have to push around before progressing. Pick up items along the way, and when you arrive on the deck, you will see two Cipher peons and the third Cipher Admin Gorigan. They speak about how the shadow Pokémon are actually made from all the Pokémon riding on the cruiser, and that they are still barely halfway through. They notice you, and one of the peons fights you while Gorigan goes away:

Cipher Peon Smarton - Cacnea 27, Huntail 27, Teddiursa 27, Koffing 27

Afterwards, a man will come out from the control room to take you back to his room, and tell you that he is actually a wanderer who stumbled upon the deserted cruiser and made it his home. You can heal at his room. He tells you of mysterious sounds coming from the bottom of the cruiser, and wants you to find out. You head down, and at the very end of the rooms find a Bonsly. It will flee however everytime you come near. Head back up to the man to tell him about it, and you can leave this place now.

However, upon leaving, you will be stopped by some Team Snagem members, and they will put you to sleep with a Gloom and steal your Snag Machine. You wake up in the man’s room again, and he’s glad that you’re ok. He tells you of a peculiar place he saw to the north, and tells you to go explore it.

Shadow Pokémon Factory:
This is where that huge pyramid thing is. The bodybuilder Zook you met in the Gateon Port will be here again, and two Snagem members are shown defeated by him. You fight him, and though discover that one of his Pokémon is a shadow Zangoose, cannot snag it because your machine’s gone.

After you beat him, Secc will send you another mail, and you head back to Pyrite.

Pyrite Town:
Back at ONBS, Secc tells you that a man called Hordel has escaped from Cipher, and is currently at the Outskirt Stand. The old man and young girl who own Bonsly will also advice you to approach Bonsly slowly, and request that you head there once more. Go back to the cruiser Libra, and approach Bonsly slowly. But a mail from Emily’s novelist mom Emma comes in to scare it, and it will run away from the cruiser. It will from then on start appearing at the Pokéspots randomly, approach it slow when you see it, and it should let you come near. After returning it to its trainer, the old man will reward with a Bonsly sheet to use at the Battle de Bingo. Back to the plot, you head back to Gateon Port to have an interview with Emma, and she will give you the amulet coin. Now, go to the Outskirt Stand.