Captain Jack Harkness, the Doctor’s former companion, is stranded on Earth and has based himself in 21st-century Cardiff to wait for the Doctor, knowing the Doctor would eventually land there to refuel with the Cardiff Rift. The Doctor lands the TARDIS in Cardiff to refuel. The Doctor sees Jack racing towards the TARDIS and dematerialises. Jack grabs on to the outer shell, causing the TARDIS to fly to the end of the universe trying to shake him off. Jack dies on the journey but revives seconds later as he cannot stay dead. As they explore the planet Malcassairo, the Doctor, Jack, and the Doctor’s companion Martha encounter Padra, a lone human running for his life from cannibalistic humanoids called the Futurekind.
The Doctor, Jack, and Martha help Padra reach a missile silo where a rocket intends to transport the last of the human race to “Utopia”. While there they meet the elderly Professor Yana and his insectoid assistant Chantho. The Professor asks the Doctor to look at their rocket engine to determine why it will not launch, and the Doctor helps him repair it and give it power. During the repairs, the Professor repeatedly hears a rhythmic drumbeat he has heard for as long as he can remember. When the rocket is ready to launch, the refugees board it. One of the Futurekind shorts the system out, filling the room with the rocket couplings with deadly radiation. Jack is enlisted to fix the couplings.
While Jack is inside working, the Doctor admits he abandoned Jack purposely because of the immortality Rose granted to Jack. Jack readies the rocket for launch. Martha unintentionally draws attention to the Professor’s fob watch, similar to the one which changed the Doctor from a Time Lord into a human. She rushes to tell the Doctor about the watch as the Professor hears voices coming from it.
The Doctor initiates the launch sequence of the rocket at the same time that the Professor opens the fob watch. A frantic Doctor runs back to the control room, but the Professor lets the Futurekind inside the silo. Chantho confronts the Professor. He responds that his name is the Master. Chantho and the Master both fatally injure each other. An injured Master stumbles into the TARDIS and regenerates into a younger form. The Master begins to dematerialise the TARDIS, stranding the Doctor, Jack, and Martha with the Futurekind.