The Pit itself (the original prison) is inside the MU, which is how people could be transported there. When the GC struck, Mata Nui crash landed on the Aqua Magna and opened up that portion of his body on impact. Once that happened and the cells were smashed, Takadox killed Hydraxon (how, dunno, but probably where the hole of the Pit was since everyone was rushing over there and it probably wasn't that big a hole. Hydraxon makes his last stand to keep the inmates in the Pit, but he gets killed.).