Stardate 5693.2: The Enterprise arrives at the last known position of the U.S.S. Defiant (NCC-1764), an area of uncharted space, to search for the missing starship. When the Defiant appears on the viewing screen enshrouded in a strange green glow, Spock is unable to scan the vessel on his sensors. Kirk beams over to the Defiant with a boarding party to investigate and finds the entire crew dead. What's more, the Defiant seems to be trapped in an interphase between two different universes. A power loss partially disables the Enterprise transporter, but the landing party manages to beam back to the Enterprise except Kirk who suddenly disappears along with the Defiant. Spock calculates that the next time to interphase will be approximately two hours, and that the captain can be rescued at that time. As the Enterprise begins to experience the same problems that doomed the Defiant: power loss, weakness and insanity among the crew, an alien vessel appears and demands that they leave Tholian

The TARDIS is in need of repair, but when the Doctor tries to track down an old friend for help he falls into the hands of Tobias Vaughn, the megalomaniac CEO of International Electromatics. The electronics company is under observation by the United Nations Intelligence Taskforce, a new international military team for fighting threats from beyond the Earth - headed by the Doctor and Jamie's old friend, Alistair Gordon Lethbridge-Stewart (promoted to Brigadier following the Yeti invasion). Vaughn is in league with aliens who intend to invade Earth, but he intends to betray them and seize control; however, as insurance should his plans fail, he wants the Doctor's TARDIS. When Vaughn kidnaps Zoe, the Doctor requests UNIT's help to rescue her - but their interference forces Vaughn to advance the invasion schedule, leaving the Doctor with little time to mount a defense... and the situation becomes more urgent when the Doctor realises that Vaughn's allies are the Cybermen, and that their army is already in place in the sewers beneath London, waiting for the signal to attack.