On Christmas Eve, Jackie Tyler (Camille Coduri) and Mickey Smith (Noel Clarke) hear the familiar sound of the TARDIS arriving at the Powell Estate in London... but are startled when the craft comes crashing down and out steps a man they have never met before, but who seems to know them -- and then passes out. Rose Tyler (Billie Piper) then exits the ship and tells them all the incredible story: the unconscious man is the Doctor, recently regenerated, his hearts still beating but somehow slipping away. As the Doctor sleeps inside Jackie's flat, Rose and Mickey head downtown for an evening of shopping, which is soon halted as the two -- and the entire crowd -- are attacked by a musical band of Santas with strange face masks that nearly kill them before they are able to get away. Back at Jackie's flat, the three take cover as the Christmas tree comes alive... a weapon designed to destroy them, for whatever's following them is attracted to them, probably because of the Doctor. Except that the Doctor is asleep on the bed, until Rose puts his sonic screwdriver into his hands and pleads for help, and he momentarily wakes up and stops the living tree. Whatever is attacking them -- the tree, the Santas now standing outside their flat -- are 'pilot fish', they learn before he passes out again. Mickey and Rose realize these 'pilot fish' are simply precursors for an invasion of a much larger force.

Meanwhile, all of Britain is watching BBC television as reports are about to come in from Guinevere One, Britain's newest Mars probe. As scientist Danny Llewellyn (Daniel Evans), leader of the Guinevere project, reports, the probe will soon send back photographs of the Martian surface. But Guinevere won't be snapping photos of Mars any time soon; it encounters a massive space-borne craft, vaguely shaped like an asteroid, which sucks it inside. Guinevere later broadcasts pictures of an alien race whose language is unfamiliar, setting all of Earth on alert and drawing Harriet Jones (Penelope Wilton), the new Prime Minister of Britain, to the headquarters of UNIT to investigate. Harriet's aide, Alex (Adam Garcia), works on a translator code to understand the aliens, while Major Blake (Chu Ornambala) of UNIT tells her that "Torchwood," a secret project, can soon be ready; Harriet, meanwhile, wonders where the Doctor is, and why he hasn't appeared to help.

The aliens make their intentions known: they are the Sycorax, and they have come to Earth to take it over and enslave its people. The Sycorax leader (Sean Gilder) teleports up Harriet, Alex, Major Blake and Llewellyn, where he kills the latter two and demands that Harriet Jones surrender in the name of the people of the Earth. In order to ensure their victory, they have fashioned a frightening weapon: they have taken over everyone on the planet with A-positive blood (due to a sample of that type of blood on the Guinevere probe as a memento of humanity), fully a third of the planet's population, and have readied them to commit suicide by jumping off rooftops. Meanwhile, back on Earth, Rose and Mickey have taken the comatose Doctor into the TARDIS, which is also teleported to the Sycorax ship; Rose and Mickey are taken hostage along with Harriet and Alex. All seems to be lost...

But aboard the TARDIS, thanks to a spilled thermos of tea...

As Rose attempts to parlay with the Sycorax leader -- an attempt that is rejected as being 'funny' -- they once again call for the surrender of the Earth... and suddenly the Sycorax language can be understood by the hostages. Which means the TARDIS translator circuits are still working. Which means that--

Out of the TARDIS steps the Doctor (David Tennant). Still unbalanced from his regeneration, still mentally unsure of what kind of Doctor he's going to be, he calls the Sycorax bluff -- the blood control was merely a hypnosis, and never would have worked as the human instinct for survival is too great. The Doctor then challenges the Sycorax leader to a duel, for control of the Earth. The Doctor and the Sycorax take up swords, a battle that continues out onto the wing of the massive Sycorax ship. The Sycorax cuts off the Doctor's hand, but because he's still within the fifteen hours of his regeneration, the Doctor simply grows a new one... and then vanquishes the Sycorax leader. He then tells the Sycorax invaders that he's won, that they're to leave the Earth and never return. The Doctor and the humans are then sent back to Earth.

As they celebrate the flight of the Sycorax ship, the Doctor, Rose and Mickey are reunited with Jackie. However, Harriet Jones learns from Alex that Torchwood -- a secret defence project based on alien technology -- is ready, and orders it to fire... a particle beam that destroys the Sycorax ship. The Doctor loses all his love for Harriet Jones, condemning her for the murder of the Sycorax, while she defends the action as necessary because he's not always around to help them. As the Doctor leaves, he plants a suggestion with Alex that Harriet Jones is 'looking tired'... a promise that he can bring her down fulfilled, as she later faces a vote of no-confidence.

As the embers of the Sycorax ship rain down on London, the Doctor, Rose, Mickey and Jackie enjoy Christmas dinner, and then the Doctor and Rose make their goodbyes... he ready to return to the great unknown out in space, and she now convinced that even with a different face and a different demeanor, he's still the same old Doctor she knows and loves.