The Doctor is being killed by Lucie.
Well, by a robot named Chloe who has Lucie's voice. He plays dead in order to fool her, and the robot is deported from their shared prison: a research center inside the core of an unstable sun. The Doctor has spent six years working on a way to keep the sun from blowing up. If it ever should, it would kill two billion people.
The Doctor was brought there by the Consensus, a war faction who intended to use the sun as a weapon once, but now try to keep it from becoming one by using the Doctor's skills. What started out as imprisonment has turned into a new reason to live for him, and although he fully realises that it may all be a giant Lotus-Eater Machine
, he tries to make the best of his new task and his self-admitted Stockholm Syndrome
. Besides, he could escape at any time if he really wanted to (he's just that clever). He's handed a new replacement robot which he names Daphne and which he gives Lucie's voice and personality again.
Soon enough, his research is interrupted by:
- The slaves of the Consensus, who claim that the computers are malfunctioning;
- La Résistance, who want to free the Doctor but who are actually in league with the slaves;
- The traitors within La Résistance, who tagged along with the rebels but who secretly want to kill the Doctor because he's more useful as a motivational martyr of legends than as a person;
- Chloe, who was actually not killing the Doctor at all but who was programmed by him to gather outside intel and retrieve the TARDIS;
- An unstoppable self-destruct mechanism; and
- Daphne, who, despite being programmed by the Doctor, is still after all a Consensus creation.
And all of the above
are lying about their intentions, about each other, and about the outside world.
In the end, Chloe tells the Doctor that the sun was never unstable to begin with, and that his six years of work has been for nothing. But when she starts shooting people, the Doctor realises that she was actually reprogrammed by the rebels when she retrieved the TARDIS. The rebels want to end the war by turning the unstable sun into a weapon of their own. Eventually, the Doctor uses the TARDIS (and three weeks of his relative time) to set his sun stabiliser system to automatic, and Daphne easily defeats Chloe with a system malfunction.
And then, Lucie Miller calls the TARDIS phone and says humanity is dying.