When you visit the Parts Shop, Perr will mention how he needs his grandfather. He's interrupted by a convenient news report about how you defeated Cipher's operation in Phenac City, after which he tells you to go get his grandfather over at Kaminko's House. On the way out of Gateon Port, you'll run into Mr. Verich and his bodyguards again. He'll congratulate you on your heroism and be off.
Once at Kaminko's House, Chobin will, yet again, mistake you for a burglar, prompting a battle.
Apparently, Chobin had a Sun Stone on his person. After the battle, the misunderstanding is cleared up, and Kaminko declares the Robo Groudon a failure, telling Chobin to do as he pleases with it. Chobin keeps it, and then asks for your P☆DA number so as to have a rematch later. He also tells you the old man from the Parts Shop is inside. Now that Chobin is outside, the door on the right he was blocking is open. Down the stairs is a series of catwalks that you move across using a crane puzzle. Just follow the matching colors and you'll find Battle CD 05. There's also an item box that holds two diary pages belonging to Jovi where she declares this area as her secret base, and decries Chobin of being a cheapskate for not letting her ride the red and blue robots. Now head back up into Kaminko's office. If you talk to him, he says that while the Battle CDs are well made, he cares not for them, so take all you find. Head for the previously locked door, and he'll tell you the R&D Lab is open, but don't disturb Makan. Inside is an elevator to the basement. Once there, you can grab a Rare Candy in the left corner before talking to Makan. You explain what's going on, and he agrees to upgrade your scooter, with both of you immediately transported to Gateon Port (Makan also takes the incomplete Robo Kyogre from the basement with him). Now you can cross the desert and head for the S.S. Libra.
As soon as you enter the derelict ship, you get a message from Justy telling you the Pre Gym has been reopened. You can head there now, or wait until later. A block pushing puzzle lays ahead, but thankfully minus having to use Strength. The first item box you see contains an Iron. You might want to save, because in the next room, up the flight of stairs, awaits a trio of Cipher goons. Gorigan is berating two peons named Snidle and Smarton about how they lost a Pokémon. Upon spotting you, Gorigan tells Snidle to handle it while he leaves. Snidle passes the buck onto Smarton, peppering his speech with made up statistics.
After the battle, a random guy who found the ship offers his bed for a healing spot. Afterwards, he asks that you check inside the hull to see what's been making some mysterious noise. Once down the stairs, on the floor you'll find Battle CD 18. Down another set of stairs is another box push puzzle, with the top item box holds a Fire Stone, and the bottom item box holds two PP Up. Down another set of stairs is yet another box puzzle, with the item box holding a Max Ether. One more puzzle awaits, with the boxes containing a Yellow Flute and TM35 (Flamethrower). In the next room is the little girl's missing Pokémon, Bonsly. Sneak up on it, all nice and quiet like...only for an e-mail to go off (Acri in Gateon Port wants to write a novel about you) and startle the Bonsly, causing it to run off. On the plus side, it left behind Leftovers. In the bottom right corner of the room is an item box with a Luxury Ball. Headed back and you'll run into your new acquaintance to explain it was a Pokémon. He'll tell you to look for it somewhere lots of Pokémon gather (in other words, at a Poké Spot). Now you can leave the S.S. Libra, but what's this?! A trio of goons blocks your path outside. They brag about how they're from Team Snagem, once feared by all (*cough*). The one wearing shades, Wakin, decides to use pragmatism to knock you out with his Gloom's Sleep Powder and steals your Snag Machine. You wake up back inside the ship...now what? Well, you can either go to Phenac City for a little distraction, or head straight for Cipher Key Lair.
If you take the elevator to the training area, in the desert section you'll find Battle CD 35. Double Team is on almost every Pokémon here, so bringing Pokémon with moves that never miss, such as Swift, Faint Attack, and Shock Wave, is highly advised. Head back up and talk to Justy to begin the matches.
As you can see, Justy loves raising his evasiveness. His party is also somehow weaker and smaller than it was five years ago. Once defeated, he gives you, appropriately enough, TM32 (Double Team) and a Lum Berry.
Cipher Key Lair
On your first visit, Zook is seen defeating Biden in a battle.
Now this looks familiar...anyway, upon arriving, you see Trudly and Folly, followed quickly by Miror B., who challenges you to another battle. Once again, thanks to Snagem, Miror B.'s ShadowNosepass can't be snagged yet.
Inside the Stand, there's a quick news report about the authorities finding the S.S. Libra. As for Hordel, tells you he rescued a Shadow Togepi from the factory, and asks that you purify it. The barman sells you items as usual.
As you exit, Secc messages you about how Snagem is hiding back in their old lair. Hordel chimes in to point out the spot on your map. Once outside the Stand, Willie will stop you and insist on having a battle.
As soon as you arrive, a message from Mayor Trest tells you that Realgam Colosseum is now open. All the teams there are Lv. 40, so make sure yours is better. For now, clean out this hive of scum and villainy. Agrev attacks you right as you enter the building.
In the upper left of the second floor, after Fudlo, you can head downstairs and find a locked box, you'll need a key to open it, so come back to this later.
If you continue south past the locked box, there is a shortcut outside, looping back to the main entrance for easy access to the healing machine.
At last, you've got the Snag Machine back. You can grab two Full Heals from the bottom corner of his office, and Gonzap also generously gives you Gonzap's Key to unlock an item box containing TM30 (Shadow Ball), head back to the bottom left section of the first floor.