I don't understand why Liquid needed Snake to activate Metal Gear...
I've always seen this as a major plothole and I've never found an explanation for it.
FOX-HOUND knew that it had two ways of activating Metal Gear; one way was by obtaining the passwords from the both the Darpa Chief Donald Anderson and the President of ArmsTech Kenneth Baker, and the other was through the use of the PAL key(s).
Since Ocelot "accidentally" killed the Donald Anderson before they obtained his password they couldn't use the password method. Thus, FH needed to use the PAL key and they knew Baker was in possession of it. So Snake meets Decoy Octopus, disguised as Anderson, who lies and tells Snake that his password had been obtained. He tells an unknowing Snake to obtain the PAL key from Baker so that he can deactivate Metal Gear (we later learn from Otacon that the PAL key acts as both an activation and deactivation key). Snake eventually obtains the PAL key from Meryl who had gotten it from Baker. Since Snake thought that the terrorists had already activated Metal Gear but it was still in fact offline, when he inserted the PAL key, he inadvertently activated it, which is what FH wanted all along.
What I don't get is... why didn't FOX-HOUND just take the PAL key directly from Baker and activate Metal Gear themselves?? When Snake does meet Baker we learn that Baker had given the key to Meryl earlier. Note they had Meryl locked up, too, right next to the Darpa Chief's cell.
They tortured Baker to try to get him to give up his password for activating Metal Gear and they succeeded, so why couldn't they torture him to get him to give up the PAL key or to get him to say that he had given it to Meryl (whom they easily could have retrieved it from while she was captured)? Note the Darpa Chief had been dead for days when Snake discovered his real body in the cell, so they had plenty of time to carry this out, with Baker and Meryl both locked away. In fact it was during this time that they conceived their plan of having Decoy Octopus pretend to be Donald Anderson and getting Snake to activate Metal Gear.
I googled this question and came across another board, and the answerer responded that the terrorists "needed Snake to figure out how to use the key." If that's the explanation I think it's very silly. Snake only figured out the temperature structure changing thing because of Otacon... are you telling me FH couldn't think to use Otacon themselves when the guy was sitting there the whole time in Shadow Moses? I mean he was one of Metal Gear's leading engineers and they must have known he was a computer whiz - it only makes sense to ask him about the key.
The worst thing is though that it was Liquid's big plan for Snake to deliver the PAL key and start Metal Gear, yet all genome soldiers and members of FOX-HOUND, Liquid himself included, tried to kill Snake throughout the game.
I'm sorry but this aspect of the plot doesn't make sense to me. If somebody could explain it I'd be very grateful.