Return to the control panel in front of Gil’s tank and insert the ADAM-infused plants into the delivery mechanism. Though you did exactly what good-guy Gil wanted from you, the part of him that isn’t so nice triggers an ambush. Numerous Splicers and no less than three Alpha Series leap into the room to attack. Immediately befriend the nearest Alpha Series and assist him in defeating one of the other Alpha Series and the Leadhead Splicers. The third Alpha Series probably won’t attack until the first two have been defeated. This gives you time to repair your Elite Security Bots and to focus. Chances are, this third Alpha Series uses a Launcher—conserve ammo by using Telekinesis to catch its Frag Grenades and throw them back.
Use the controls to perform the genetic extraction and retrieve the Genetic Key that is generated through this process. This key opens the secret entrance to the place where Sofia Lamb is keeping Eleanor.
As for Gil, the choice is yours. His pre-recorded messages instruct you to hit the disposal button and flush him out to sea, but the present-day Gil begs for your forgiveness and wants to live. The choice is yours.