The planet they were on was a forerunner shield world which essentially uses a stationary slipspace field to preserve everything inside of it. The villain is the didact a forerunner preserved in this shield world. He is pretty much a war criminal of the forerunners who wants to take over the universe. When the chief sets off the nuke to kill him Cortana uses the final parts of her that aren't currupting to aces the teleportation network and teleport the chief away from the explosion to say goodbye to the chief with her remaining sane processes. That's pretty much it I'd play the story agaib to get more in depth.