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The Big Bang Two refers to the explosion caused by the doctor "rebooting" the universe after its destruction, in the TV episode The Big Bang.
In 1996, all stars in the universe had gone supernova due to the unique circumstances of the TARDIS's destruction, At that time, the entire universe had already been destroyed except for the Earth and its moon. The TARDIS's continuing explosion, which (like the resultant destruction of the universe) was happening "at every point in history," acted as a replacement for the sun.
When the Pandorica opened in 1996, it contained billions of atoms from the universe as it should have been, which had a restorative effect on a fossilised Dalek. This was "impossible" because the Daleks had never existed, having been wiped from history, so there should have been nothing to resurrect. The Doctor reasoned that if the Pandorica interior's energy field could be transmitted to the entire universe, this would recreate the universe.
The Doctor used a Vortex Manipulator to fly the Pandorica directly into the heart of the TARDIS's eternal explosion. Since the TARDIS was exploding at all points in history, the particles and restorative energies from within the Pandorica were scattered at every point in time. A new universe was created based on the old one, but with the Doctor (briefly) having never existed. "Rebooting" the universe, minus the Doctor and the events of Series 5, caused this new universe to proceed undamaged, because the TARDIS had not exploded.
Potential Controversy
Because this new universe's survival hinged on certain omissions when compared to the history of the prior universe, it's unclear whether any previous Doctor Who adventures ever took place. It's somewhat likely that all prior stories were remembered back into existence alongside the Doctor himself, however, this would conflict with removing the cracks. The opposite alternative would be if no prior adventures took place, which would drastically alter history and the status of many characters and factions.