Chapter 3: The End
The Doctor made his way back to Gallifrey; he walked into the board room which was now deserted seeing that everyone knew now that the Daleks had the cruciform they would attack Gallifrey first, so they all hid in underground bunkers, just hoping to survive. He opened the safe with his voice recognition; inside the safe was the Time Deductive bomb. He took it out, he defined it so that it would only destroy Time Lords and Daleks, he then tried to define it to only destroy Daleks but he didn’t have enough time. He knew that he would be safe because he was at the eye of the bomb and this bomb would destroy all history of the Daleks and the Time Lords by tracking their biology, maybe he could find Susan and tell her to come in the Tardis so she too would be at the eye of the bomb and therefore protected but there was no time. He pressed the button on the bomb and watched Gallifrey and Skaro burn from time. The explosion sent shockwaves to many planets therefore destroying them but only in their present time, but the shockwaves sent the Tardis crashing into Earth which is where the Doctor was badly hurt and regenerated into the 9th Doctor, when he finished regenerating several tears ran down his face.
In the episodes Bad Wolf/Parting of the ways the Dalek emperor and his ship were falling through time at the same time this story happened and so they were unaffected.
The Cult of Skaro and the Genesis Ark were in the Void and so they were unaffected.
The Master changed his biology after the Daleks got the Cruciform and therefore wasn’t recognisable as a Time Lord and was unaffected.
This story was created by me and is trying to explain the Time war.