This article is incomplete. Please feel free to edit this article to add missing information and complete it. Reason: Missing movesets and confirmation of abilities for Cipher R&D Mesak, Morbit, Elrok, Coffy, and Tekot.
Immediately upon entry to the Cipher Lab, you'll find the car that the gang took Professor Krane in. That probably means Professor Krane is here. Also immediately, six Cipher Peons in different colors appear. You only have to face one of them, but I'd recommend facing all six to raise your levels and catch all their Shadow Pokémon.
After the battle, get the Revive and go upstairs. You'll see a cutscene with a really-long-haired Cipher female, Naps (the guy you got the Teddiursa from), and Professor Krane! After the cutscene, telling you about a mysterious "XD001" the girl wants help with, head south and another Cipher Peon appears.
Keep heading along the set path to fight two more Peons. Cipher Digor is optional by going up the elevator to the right, but by fighting him the player has access to a healing machine and a box containing 1 Ether.
In the next room, you'll hear two scientists talking about the Grand Master of Cipher. Could it be Evice from the last game? Nope, they call him "Greevil". One of them will spot you. The other won't battle you.
After the battle, check the table for the ID Card and a Great Ball to the right. Go north for the elevator and then keep going north and up the elevator then south and you'll be able to heal up. Go back north of the healing machine, down the elevator, first left, through that hallway and you'll use the ID card to get in an elevator. Tekot is an optional battle depending on the route taken.
Finally, Professor Krane is free and will join your party. Don't forget to grab the Leaf Stone and then scram!
Cipher Admin Lovrina
On your way out, of course, R&D Tekot and the girl will appear and stop you. The girl's name is Lovrina, she's a Cipher Admin, deny her offer, and on with your first real boss battle.
Now that you're free, bring Professor Krane home to the Pokémon HQ Lab.
Pokémon HQ Lab
The Purify Chamber has been completed. After getting a walkthrough on it, purify any ready Pokémon.
Your mother asks you to check on a guy named Datan upstairs. You know, the guy that's sitting at the computer. But he's not there. He's actually outside. Talk to him, Professor Krane will appear, and he'll tell you to send the Data ROM to Pyrite Town. Now you're on your way to Pyrite Town!