The Valeyard (He Jests at Scars...)

In one timeline, the Valeyard succeeded in killing the Doctor in the Matrix, gaining his knowledge and obtaining immortality. He created Chronopolis, a city within the Time Vortex around his TARDIS, which protected it from harm. The Valeyard placed a sample of every extinct species within it. Initially the Time Lords were willing to let the Valeyard exist as an object of potential study, some believing that his lack of morality would make him a more effective 'agent' than the Doctor, but his obvious interest in chaos for its own sake- equally willing to avert the creation of the Daleks and have humanity make contact with the Silurians as to leave Earth at the mercy of the Vervoids- eventually forced the Time Lords to recognise the dangers of letting the Valeyard roam free, albeit too late to stop him recovering the Doomsday Weapon and turning it on Kasterborous.

However, a great deal of this was an illusion: The Valeyard had travelled in time interfering so much in the lives of his past selves that he had radically damaged Time. He was hiding in his TARDIS, which had generated various force-fields to keep him immobilised, afraid to take any action lest he make things worse. The TARDIS generated the fantasy of Chronopolis to make the Valeyard feel safe. Mel became trapped with him, and the two were frozen in Time, possibly forever. Interestingly enough, The Valeyard at the this terrible end gained respect for The Doctor, referring to his greater wisdom and experience, recognising that the Doctor sometimes avoided taking action because it was more practical rather than because he was afraid. Furthermore The Valeyard finally saw the damage his actions had done, using his last words before being frozen to apologise to Mel. (NOTDWU: He Jests at Scars...)