I always thought that episode 79 and 80 are very confusing, both because there is a lot happening and because you're given some very confusing information, so I will do my best to explain them further.
A short summary of episode 79: Not-Sasha is chasing Jon. Jon took Michael's door to escape, and it let into the tunnels under the institute.
Martin and Tim went into the tunnels to look for Jon, but found Not-Sasha instead. Running from that, they ran into Michael, and when trying to escape Michael, they went through a door. Uh-oh! That door wasn't there before! They are trapped in Michael's corridors now.
Jon was walking through the tunnels, and picked up a metal pipe to protect himself (like that was gonna do anything). Not-Sasha caught up to him, but right when it was about to get him, the walls moved to trap it, and a mysterious voice said "Mr Sims. I think it's time we had a talk."