Dark Pokemon Lab:
Use the main key to open the door. Enter the right building and its right control room to switch off the lock of the left building. You cannot move further in the right building yet, so leave and enter the left building. You'll fight a researcher:

Researcher - Rabon - Voltorb, Voltorb

He drops the card key for the right building and you pick it up to enter the innner part of the right building. You find your way down to the main control room and fight various Cipher battlers and researchers. You have to pick up 3 DNA samples scattered around the place:

Cipher Peon - Cole - Aipom (Dark 43), Remoraid, Furret, Castform
Researcher - Bika - Magnimite, Electrike, Chinchou
Researcher - Perim - Voltorb, Magnemite, Magneton
Researcher - Daruru - Voltorb, Magnemite, Magneton
Cipher Peon - Lare - Nuzleaf, Hounder, Carvahna, Murkrow (Dark 43)
Cipher Peon - Vana - Swablu, Pupitar, Forretress (Dark 43), Swablu

Cipher Peon - Lesar - Ariados (Dark 43), Rhyhorn, Grovyle
*Pick up DNA Sample next to this battler

Cipher Peon - Tanie - Linoone, Granbull (Dark 43), Vigoroth
*Pick up DNA Sample

Researcher - Nicola - 2 Electrodes
*Pick up DNA Sample

Researcher - Aren - Electrode, Magneton
*He will activate the alarm after you fight him

Cipher Peon - Remil - Vibrava (Dark 43), Swellow, Kadabra, Kecleon

You grab all DNA samples, go to the DNA machine to reveal their pokemon identites and remember them. When you go back to the door Cipher Remil is guarding, you have to pick the three correct pokemons to open the door. Open the door, and fight another Cipher battler:

Cipher Peon - Skrub - Graveler, Wobbuffet, Clamperl, Medicham

Then you head down to find Ein deleting the dark pokemon data. He fights you:

Cipher Admin - Ein - Huntail, Altaria, Lanturn, Golbat, Raikou (Dark 40)

Beat him and he flees. You then receive a mail from Sureddo telling you about valuable date from the lab and you pick up the DataRom from Ein's table. You also find the last Ein File titled L, explaining their plan to create one darkest pokemon. You head back to Sureddo in The Under.