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 downstairs. 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 can get 1 Ether
Cipher Peon Digor
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. (I didn't run into this Tekot trainer, but someone else righting this guide ran into them, following my route you avoid Tekot and run into Naps).
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!