We ended the previous episode with what looked like the execution of the Doctor, so his being dead could be a real problem going forward.
Fortunately, he isn’t dead. His body is fine but hidden, and his mind was sucked into the Matrix by the mysterious Renegade. Renegade wants the Doctor to promise not to interfere with whatever vague plans the Renegade has as he tries to reform in the matter world, a place he says he used to live in. That’s still a bad idea, the Doctor knows this, and he also knows this Renegade is probably up to no good, so he refuses.
Fortunately, the Doctor still has allies in the outside world in the form of Nyssa and Damon the technician can look into more and find evidence that points out that yes, someone on the Time Lords Council did do whatever it was was done with the Doctor’s genetic code. The Doctor couldn’t have, and Damon didn’t tell the Castellan about it because, well, the Castellan’s on the Council and how would Damon know whether or not the planet’s security chief was in on the plot or not?
For what it’s worth, the Castellan and Commander Maxil are looking into the crime because something doesn’t quite add up and they come very close to figured things out. Of course, like any good conspiracy theorist, the Castellan refuses to believe the Doctor isn’t involved, but both he and Damon realize the Doctor isn’t dead and someone is hiding the Doctor’s body. Granted, they have different ideas on who is responsible and the Castellan still thinks the Doctor is involved, but the Doctor is just floating alone in the void of the Matrix until he changes his mind about helping the Renegade. And the Doctor isn’t interested in doing something like that.
You know, until the Renegade captures Tegan in Amsterdam and uses her to force the Doctor to promise not to do whatever it is the Doctor always does. See, by sheer dumb luck, someone the Doctor knows and cares about managed to find the Renegade’s home base on Earth completely independently and on her own. And since the Doctor cares, that plan works and he’s removed from the Matrix.
But the Castellan and Maxil are looking for him now. Good thing he finds Nyssa and Damon first, and he can maybe save Tegan if he can get to the TARDIS in time, but Damon says a few vital parts were transported out at some point. The bigger problem is someone on the High Council is allowing the Renegade to maybe have full access and control of the Matrix, and nothing good will come of that. Plus, it looks like the President did it.
Eh, it was Counselor Alfred. The friendly one. The Doctor finds him trying to force the President to help the Renegade at gunpoint because, well, he says the Renegade is a force for good. That doesn’t seem likely, but then Alfred takes a blast from a security man intended for the Doctor.
See, by then, it came out who the Renegade really is: Omega, one of the first Time Lords, a guy who invented time travel and was driven insane because no one knew he was still alive in an antimatter universe. Oh, and now he has control of the Matrix. That’s bad.
Especially since the last time we saw the guy, it took Three Doctors to stop him.