I'm afraid I can't remember everything that was done in the Machine criticals; certainly not which missions did what. Here's what I remember, though:
Agent Gray told us to put our investigations into the Assassin on hold for a moment to deal with another matter. Zion were not just awakening bluepills who wanted to be awoken, but also extracting bluepills who didn't, people who didn't have a clue what the Matrix was, who didn't know what was going on. In order to counter this, we were ordered to replace a prototype for some sort of medicine with a Red Pill, which would then get mass produced and bought by a number of Matrix denizens, thus bolstering the number of Machinist operatives.
(As a side note, this would seem to indicate that a lot of NPC redpills are recruited by the Machines immediately upon extraction, whereas everyone who plays this game starts out with Zion.)
Before that, though, we had to investigate how Zion were orchestrating all these mass awakenings. Turns out they were sending out spam e-mails! When we got to the place from whence they were being sent, we encountered a bunch of Commandos (the General's men) investigating the issue themselves. They claimed to be on our side, or were at least interested in helping us.
In a later mission we had to escort one of the Commandos to a safe house where he would be questioned by Agents. When he got there, though, he somehow committed suicide.
Oh yeah, and it turns out the Commandos were interested in jacking-in technology (or something to do with the interface between human and Matrix). We planted false information for them to find.
Message Edited by [TGS]Procurator on 10-06-2005 09:14 PM