Straxus seemingly dies by helping the Doctor and Molly escape. The Eighth Doctor and Molly ignore the coordinates programmed into the TARDIS by Straxus and instead end up on the planet Srangor, where Straxus previously tried to kill himself
. Interestingly, Molly is now able to understand alien languages. They happen on Straxus' assistant, dying, who — before passing away — reveals that regeneration is impossible on Srangor due to a radiation mishap.
Straxus turns out to be still alive, and confers with the Lord President of Gallifrey about their plans to deceive the Doctor. His assistant sacrificed himself to trick the Doctor. And Eight ignoring the pre-programmed TARDIS controls was exactly what the Time Lords expected, so they programmed the TARDIS specifically to activate
and vworp to the pre-programmed spot once the Doctor would deviate from the programming.
Molly, however, falls straight into the Dalek headquarters and seemingly to her death. She's immediately captured. A local named Nadeyan, who previously watched Straxus' attemps to kill himself
, takes care of Eight and helps him deal with the trauma. Nadeyan lost his entire family to the Dalek occupation of his planet, but he tries to live a normal life as best he can.
Kotris, meanwhile, extracts Molly's memories and works out that she's full of MacGuffin
bits ("retrogenitor particles") that will be implanted into her by Kotris in the future, as he and the Dalek Time Controller are using Gallifreyan technology to build an all-seeing temporal chamber... thing. Eight and Nadeyan end up in said chamber, in its first stage of construction. They meet up with Molly again, and escape in the TARDIS, which is rather mysteriously right next to them all of a sudden.
The Dalek Time Controller and Kotris watch all that happen from the future, using the temporal chamber, which the Doctor was unable to interfere with — and note that the Time Lords were responsible for saving the Doctor, thus enabling the temporal chamber to be completed. But Kotris now has a new memory, namely that of meeting Molly centuries before and learning that he would one day fill her up with retrogenitor particles. Molly, struggling with Mind Probe
-induced amnesia and Loss of Identity
, decides that if she's the key, she might as well just throw herself into the Time Vortex. That way, no one can use her eyes anymore to view the Doctor's trajectory. She's had a good life, a fantastic friendship with Kitty, and she's saved the lives of many a soldier. She's been familiar with death all her life, with most of her brothers and sisters having died already. She's fully ready to commit Heroic Suicide
, but the Doctor talks her out of it, unable to cope with the idea of another companion dying.
While the Doctor realises that the controls of his TARDIS are suddenly very "bog-standard factory settings", Nadeyan finds the Doctor's real
TARDIS inside the TARDIS they're in. Which turns out to have all its defenses ripped out, leaving them vulnerable to a Time Ram used by the Daleks. The Doctor and Molly are taken captive and finally meet Kotris and the Dalek Time Controller, although Nadeyan manages to escape. He meets Straxus deep inside the Doctor's real TARDIS.
Working together with the Dalek Time Controller, Kotris injected baby Molly with the retrogenitor particles, knowing that they would activate if she came near Time Lords. This would eventually allow Kotris to turn the evolution of Time Lords backwards
, erasing them from existence. To avoid this fate himself, Kotris first had himself genetically altered to become something much closer to the Daleks than to the Time Lords. However, Straxus is busy changing the timeline — he swapped the particles when the fake TARDIS landed near the projector, changing them to a setting that will instead un-evolve the Daleks
once activated. He promises Nadeyan a new timeline in which the Daleks never existed, never invaded Srangor, and never killed Nadeyan's family. The only person that needs to die is Molly. Nadeyan won't have it, punches Straxus in the face
and sets out to save Molly, because no matter how much the loss of his family hurt him, it's not worth destroying the life of one more person.
While Straxus attempts to activate the particles and erase the Daleks from history, "Kotris" turns out to be a future incarnation of Straxus, who eventually became horrified by the Gallifreyan way of life and decided to engineer a Last Great Time War all of his own. In a grand Heroic Sacrifice
, Nadeyan destroys the device and himself with it. Young Straxus gives the Doctor a grand What the Hell, Hero?
speech for essentially saving the Dalek race. It turns out that the Lord President of Gallifrey found out about the plan, broke all laws of time and ordered Straxus to commit Heroic Suicide
on Strangor, where it was the retrogenitor energy itself that prevented regeneration. But Kotris saw it coming and, to preserve his own timeline, prepared temporal drones that would prevent Straxus from killing himself no matter where he'd attempt suicide. Straxus still has zero desire to regenerate into a "psychotic moron", but it doesn't matter much anyway, since the Dalek Time Controller decides to exterminate Straxus before he can regenerate into Kotris in the first place. The events will fade, but the Dalek Time Controller, who has developed a perfect Ripple-Effect-Proof Memory
using Kotris' methods, will exist outside of any new timeline anyway.
Molly decides to return to the battlefields of France, as a re-written timeline means that the Daleks never attacked — and her lady Kitty is still alive.