At the end of Zagreus, the Doctor is himself infected by Zagreus and struggling to maintain control. He and Charley leave this universe for the Divergent Universe, where time does not seem to exist as such, and so Zagreus' anti-time energy is powerless.
After a series of adventures there, the events of The Next Life take place. (Spoilers follow.)
In the Divergent Universe, Zagreus has left the Doctor and manifested itself as a new being, a woman called Perfection. She and Rassilon (who created the Divergent Universe in the first place) attempt to use the Doctor and his companions to help them escape back into the Doctor's Universe, but they do not succeed. The Doctor and his companions escape into the TARDIS and return home, leaving Perfection/Zagreus and Rassilon behind.