The Doctor's nemesis the Master has taken control of the planet Siralos, which is made of "pure psychic energy". With this planet's power, he plans to mould the universe into his will. To begin, he takes the first seven incarnations of the Doctor out of time and space and puts them in the Determinant, a domain he has created from the conquered will of Siralos. He plans to eradicate any trace of the Doctor from time and space, so he may be free to rebuild the cosmos as he pleases. However, the player's character, the Graak (a psychic being created by the Doctor), pledges to stop the Master's plans, and the game begins.
The Graak is an intelligent, psychic and seemingly altruistic organism, turquoise in colour and resembling a jellyfish. It floats about four feet from the ground, and has no visible organs nor any recognizable features. The Master states that the Graak is protoplasmic. Although it has no limbs, the Graak is dexterous enough to be able to handle items such as a sonic screwdriver and a radio transmitter. It only speaks when it asks the Doctor questions as part of a challenge, and has a high voice varying in tone and inflection (implying that speaking is a strain). When the Master calls the Graak "a good little doggie", it is heard to bark.
It is a matter of debate as to how the game fits into the continuity of Doctor Who. There are references to the "seven complete incarnations of the Doctor", with no reference made to either the Eighth Doctor, despite the game being released some time after the 1996 TV movie. However, the TARDIS database does vaguely mention the Seventh Doctor's regeneration. It has been speculated that the Master's imprisonment at the end of the game is by the Daleks, which would then lead into the opening of the TV Movie. This could also explain the absence of any mention of the Eighth Doctor (if the events of the game are set before the TV Movie).
Gameplay
The bulk of the game takes place in the Doctor's TARDIS (and, on occasion, the Master's TARDIS, reached via "junctions" between the two time machines). The game begins in the Console Room of the Fourth Doctor's TARDIS, and the player must then select one of the Doctor's seven incarnations and activate the TARDIS to go in search of them.
Upon reaching the TARDIS of the selected Doctor (and also before almost every puzzle in the game), the player can use a "Time Winder" (a pyramid-like save point) and then set out into the TARDIS to find the Master (and, accordingly, the Doctor).
Upon leaving the Console Room, the player, as the Graak, must find the Great Divide: a chasm which separates the TARDIS from the Determinant. However, the Master has placed several of the Doctor's enemies in the TARDIS to make things more difficult for the Graak, such as Daleks, Cybermen, Autons, Ice Warriors, Quarks, Sea Devils, Silurians, Sontarans, Yeti and Zygons. There are weapons and implements in the TARDIS that can be used to incapacitate or kill these monsters, some of which can be kept throughout the quest (such as the sonic screwdriver, or a radio used to contact Brigadier Lethbridge-Stewart for advice and hints), and others which can only be used for a limited time (such as Dalekanium and watering cans).
Upon reaching the Great Divide, the player selects a symbol and the Master gives the Graak a riddle. During the loading time, a map of the area of the TARDIS the player will explore is shown. The Graak will have to complete a certain objective (e.g. perform the Doctor Who theme on floor tiles), find certain information on monsters or Doctors (either from the Doctor's "City of Thoughts" database in his TARDIS or from the Master's "Monster Database"), or collect an item (such as a Stattenheim remote, or a Nestene Consciousness control sphere). Whilst the player is scouring the TARDIS(es), they may use telepathic links with the Doctor (resembling the TV title sequence effect of the Third Doctor's episodes) and the Doctor will give a short clue to the player. Having completed their task (out of a possible 28 tasks), the Graak then returns and gives the Master the item, or crosses a grid of tiles, or selects the true Doctor out of three possible choices, or similar. If the player fails, they will have to begin again (from the nearest Time Winder). If they succeed, they will have to face the Master in the Determinant. If they defeat the Master, that incarnation of the Doctor is freed:
First Doctor - A chase around the Celestial Toymaker's toybox (with Quarks)
Second Doctor - A race against the Master on London Underground trains (with Yeti)
Third Doctor - Seek and destroy the Dalek spaceship
Fourth Doctor - Search around the maze that is the Doctor's mind (with Raston Warrior Robots)
Fifth Doctor - A joust in a medieval ring against a Sontaran on a hoverbike
Sixth Doctor - Search the icy wilderness of Mars to find the Doctor
Seventh Doctor - Race against the Master's car in the Doctor's Edwardian car, Bessie (with Autons)