Plot

Following the Master's trial and execution at the hands of the Daleks, the Doctor, currently in his seventh incarnation, is transporting the Master's remains to Gallifrey via his TARDIS. En route, the box with the remains breaks open and an ooze leaks out, infecting the TARDIS. The Doctor is forced to make an emergency materialisation in San Francisco's Chinatown on 30 December 1999.

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As he exits and locks the TARDIS, the Doctor is shot by a gang chasing down Chang Lee, a young Chinese-American man. Lee calls for an ambulance and escorts the unconscious Doctor to a hospital, unaware the ooze from the TARDIS has gotten aboard. At the hospital, cardiologist Dr Grace Holloway attempts surgery to remove the bullet but is confused by his strange double-heart anatomy, and accidentally lodges a cardiac probe in the Doctor's body, apparently killing him. The Doctor's body is taken to the morgue, while Lee is given the Doctor's possessions including the TARDIS key. Meanwhile, the ooze takes over the body of the ambulance driver, Bruce, transforming him into a new body for the Master.

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Later, the Doctor's body regenerates, and the new Doctor, suffering amnesia, gathers clothes from remnants of a recent party. He recognises Holloway, who has resigned from the hospital after the failed operation, and follows her to her car, proving to her he is the same man by pulling out the cardiac probe. Holloway takes him home to recover. Lee returns to the TARDIS where the Master arrives and puts him under his mind control by claiming the Doctor had stolen his body. The Master convinces Lee to open the TARDIS and then to open the Eye of Harmony within it, which requires a human retinal scan. When the Eye opens, the Doctor is flooded with memories and realises the Master is searching for him, and tries to block the scan. He warns Holloway that while the Eye is opened, the fabric of reality will weaken, and potentially destroy the Earth by midnight on New Year's Eve if they cannot close it. However, he needs an atomic clock to do so, and Holloway finds one on display at the San Francisco Institute of Technological Advancement and Research.

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Outside, they find the ambulance with the Master and Lee waiting for them, offering them a ride. The Doctor does not immediately recognise the Master, but discovers his true identity en route, and he and Holloway escape, but not before the Master can spit an ooze-like substance on Holloway's wrist. The two continue to the Institute and obtain the clock, returning to the TARDIS. The Doctor installs the clock and successfully closes the Eye, but finds the damage to reality too great and that he must revert time before the Eye was opened to prevent the destruction of Earth. As he connects the proper TARDIS circuits to do this, the Master remotely takes control of Holloway's body, causing her eyes to become inhuman, and she strikes the Doctor unconscious.

The Doctor and the Master in their climactic battle

The Doctor wakes to find himself chained above the Eye, the Master poised to take his remaining regenerations while Lee and Holloway watch. The Doctor is able to break the Master's control on Lee, and Lee refuses to open the Eye for the Master. The Master kills him, and then releases his control on Holloway to return her eyes to normal. He forces her to open the Eye and then begins drawing the Doctor's life-force. Holloway, under her own control, is able to complete the final circuits to put the TARDIS into a time-holding pattern, preventing Earth's destruction, and then goes to free the Doctor. The Master kills her, but this has given enough time for the Doctor to free himself and attack the Master. The Doctor gains the upper hand and pushes the Master into the Eye. The Eye closes and time reverts a few minutes, undoing Lee and Holloway's deaths.

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With no further risk to Earth, the Doctor prepares to leave. Lee returns his possessions, and the Doctor warns him not to be in San Francisco on the next New Year's Eve. The Doctor offers Holloway the opportunity to travel with him, but she politely refuses, and instead kisses him goodbye. The Doctor departs alone in his TARDIS.