The Valeyard (He Jests at Scars...)

 was a distillation of the Doctor's dark side. He 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.

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, 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. (NOTDWU: He Jests at Scars...)