Picking up the story, it turned out that the Second Doctor and his friends had ended up in the midst of war games where humans were plucked out of time and were fighting each other as part of some nefarious alien plot, while thinking they were still fighting the wars they had been plucked out of.
In this second disk the action moves from within the war games themselves to the alien headquarters. The Doctor goes back and forth with the menacing aliens, along with the one person working with them who is actually from The Doctor’s own people. All this plot stuff though is basically all just to set up the ending though. This is the last Second Doctor story.
So basically, at the end of the main part of the adventure here, the Doctor realizes that the only way to undo the mess that has been caused is to call his own people into the situation, to have them clean things up. Of course, there is the problem that he is a fugitive from his own people. Basically, the Time Lords have a policy of non-intervention in the affairs of other people. The Doctor chafed under those restrictions, stole a Tardis, and then traveled the universe getting involved with things interfering all the time (to make things better). As such, he was an outlaw. In any case, calling in the Time Lords mean that the Doctor himself is caught. He is given a quick show trial, then is sentenced to a regeneration (although they didn’t call it that yet) then exile on Earth. (His companions are made to forget all but their first adventures with the doctor and are put back where he picked them up.) And thus ends the Second Doctor.
The regeneration at the end… well, the start of one, you don’t actually see the transformation into the Third Doctor, is the main point of interest in this whole adventure. Otherwise it is a bunch of running around, although it has a few funny Second Doctor moments.
Oh, and Amy and Brandy were really amused at the faces some of the bad guys made as they hypnotized people at various parts of the story. That was indeed funny.