That was never explained.
I think we're meant to assume it was one of the Silence (they seemed to change the voice between episodes). The Silence trying to kill the Doctor by blowing up the TARDIS (to prevent The Question from being asked at Trenzalore) inadvertently caused the cracks in time. Their other attempts to kill the Doctor were of course Lake Silencio and the Judas Tree poison. As time isn't linear, particularly in Moffat's Who
, it may be that these attempts, from the Silence's perspective, didn't happen in the same order that we saw.