When first entering the tunnels on level 9, player receives a keypass from the guard that is necessary for entering the outer door (i.e. when returning).
I had no problem making my ways to and from the tunnels for the first two and a half quests. I completed the "Capture Hoppers" mission, took them back, then was sent out again to find Newton. I found Newton in the caves, told him it was safe to go home, and then started returning myself. At some point my keypass disappeared, and I could not enter the antechamber (with the bioscanner) that precedes entry back into the complex.
Unfortunately I don't have a save point before losing it. I have not developed a habit of creating intermittent new save files - that will change now! Anyway, unless someone has a suggestion for how I can avoid restarting.... this will at least serve as a record.
