Well, that was all a confusing mess. I'm not sure which story the author was attempting to tell but neither of them was terribly coherent.
The Lenny Henry story is simply that he was a terrible human who decided to make an alliance with aliens. The purpose being to wipe all human DNA and be rid of them. To get back at his mother. No other motivation. Really doesn't seem worth it by the end.
And then the new Master. Who is mad that all of Gallifrey's history is a lie. That all Time Lords know but can't remember. But the Master can remember so he wipes out Gallifrey again (didn't last too long this time) and then he wants to wipe out the humans. Just to let the Doctor know how upset he is, but won't exactly say why. Maybe they've decided he's half-human on his mother's side? I've got a feeling the next producer will need to forget this Time Lord stuff ever happened.
And the two stories team up because they have common goals?