With a anti-matter being trying to enter the universe through the Doctor, the Gallifreyan high council see's only one clear course of action. They decided to put the Doctor to death in order to prevent the occurrence.

The Doctor having returned to Earth, finds Omega's Tardis and is not able to prevent Omega's transfer upon arrival. Omega being of anti-matter and unstable is on the verge of destroying the planet in his attempt to regain a body.