The year is 2056. Earth now knows of the horrors in space and knows it's time to defend themselves.
The United Nations trys to fight them, but they fail. Torchwood secretly fight the aliens, giving the UN the impression that they are winning. But Torchwood listens to no one. No one except their leader, Captain Jack, and the one who he listens to.

Captain Jack answers to no one. No one except the one who left him on a space station, millions of years in the future. The Doctor.

Torchwood 1, London. Only recently rebuilt due to circumstances.
Torchwood 2, Edinburgh. Steadily growing members.
Torchwood 3, Cardiff. The Torchwood head base, under command of Captain Jack.
Torchwood 4, unknown. Still missing.

The Doctor, come to Earth to find a companion is now caught up in the new time war, and is forced to work alongside Torchwood and Captain Jack to help save the Planet. Together, they fight off the alien invasions, one by one.