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1 - Arrival
Your objective here is to infiltrate Saren's research facility and disable the AA guns so that the Normandy can drop off the nuke. Keep moving.
2 - Security Console
This console will grant you access to the facility's security system. You have two choices - cut the alarms to make infiltration a little easier or trigger the alarms on the far side of the base to make things a lot easier for you (since it will draw the attention elsewhere). The latter approach will bring the guards toward Kirrahe, though, which may be more than the Salarian teams can handle. If you choose to take on the guards yourself, you'll earn several Paragon points. Send them Kirrahe's way and you'll earn several Renegade points.
3 - Warehouse Defenses
The warehouse is defended by two Geth Destroyers, a Geth Shock Trooper, and some "Indoctrinated" Salarians.
4 - Geth Juggernaut
At the top of these stairs, you'll encounter a Geth Juggernaut that will make your mission a little tougher for a minute or two. When it's down, replenish your Megi-gel stock at the aid station and then head through the doors leading to the security office.
5 - Indoctrinated and Loot
Kill the two Indoctrinated here, then grab the items inside the crate and hardened weapon locker before continuing on.
6 - Detainment Cells
These stairs lead down to Cell Block A of the detainment level, where you'll meet Lieutenant Ganto Imness of the Third Infiltration Regiment. The Salarian Commando was captured during recon and can brief you on the indoctrination experiments Saren has been performing. If you want, you can let him out of his cell for two Paragon points.
Once Ganto is gone, you can either free or kill the "docile" Salarians in the next cell. More Paragon or Renegade points await you following this decision.
7 - Exit to Labs
This elevator will take you up to the Genophage labs area of the
Virmire: Labs map.
8 - Exit to Labs
These stairs will take you up to the Cell Block B section of the
Virmire: Labs map.
9 - Storage Room
If you use the stairs on the south side of Cell Block B on the
Virmire: Labs map, you'll reach this storage room. There are two Indoctrinated and an aid station here, as well as stairs down to the detainment level where four crates can be looted.