After Neosekken's confrontation with Psycho Mantis, he moves on past the commander's room and into some caves that lead the way to the communication towers, with Meryl continuing to accompany Snake. The caves aren't a walk in the park however, as they are inhabited by wolf dogs that are not too friendly with Snake. When Neo makes it through the caves, he finds himself in front of the communication towers, but before he can even get close to them Snake and Meryl are ambushed by FOXHOUND member "Sniper Wolf", the group's best shooter. Meryl is shot several times by Sniper Wolf, and is left immobile on the ground between Snake and the towers, and if Snake tries to go and help her he'll just be picked off by Wolf.
Not having a sniper rifle of his own to fight back with, Neo has Snake call Otacon to find out where on the base he can find one, and is told that there is a sniper rifle all the way back at the armory of the tank hanger. With no other options available to him, Neo is forced to retreat and go back for the sniper rifle, leaving Meryl behind. When he eventually gets back to the armory and finds the sniper rifle, Neo rushes back to the communication towers to try and save Meryl, only to find that the only person there waiting for him is Sniper Wolf.
Neo battles Sniper Wolf in a duel and eventually wins, and in order to find out what happened to Meryl Neo has Snake travel to Wolf's location to try and interrogate her - only to find himself walking head-first into a trap set up by Wolf. Snake is captured by the enemy. Waking up in what appears to be a torture room (one that looks like a room Neo saw in an earlier flashback), Neo and Snake finally come face to face with the leader of the terrorist plot: Liquid Snake. Liquid claims that he and Snake are both the last surviving sons of Big Boss, but before Liquid can go into more detail he is called by Vulcan Raven and informed that the U.S. government is not responding to the their demands. Suspecting that something is off with the situation, Liquid leaves, promising Snake with no small degree of venom that they'll see each other later.
It is then that Snake finds himself at the mercy of Ocelot, who begins using electric torture to try and pry information out of Snake (and also just to make the guy suffer just for kicks, because the guy's a sadist. But don't tell Ocelot that, because apparently sadists are just "uniformed fools".), while also raising the stakes by leaving Meryl's fate in his hands. Specifically. if Snake (Neo) gives up for any reason during any of Ocelot's torture sessions, Ocelot will put a stop to them but will promise to slowly kill Meryl in Snake's stead, but if Snake (Neo) wants to keep her alive then he'll need to stay strong and survive each torture session he's put through.
Neo survives the first round of torture and it put into a nearby cell, where he finds the corpse of the DARPA Chief - only it appears that he's been dead for at least several days rather than several hours when he died right in front of Snake, although this is far from the only mystery that is plaguing Snake and Neo's minds. Snake is then called by his support team, and it is then that several topics are discussed and with them more revelations are had as to what exactly is going on with this entire incident, along with learning more about Snake and Naomi's pasts. After these conversations come to an end, Neo begins formulating a strategy he can employ to escape his cell. And eventually, with Otacon's help, he manages to do just that...
