The Doctor and Jamie have temporarily departed from Victoria as they set out on a mission from the Timelords. Detecting dangerous time experiments, the Timelords have unofficially sent the Doctor to see what he can do to halt the experiments. The Doctor hopes it's a mission that'll go over easy. But despite knowing the station director, Dastari refuses to halt the experiments. To make matters worse, Dastari is collaborating with a pair of Androgums. Shockeye, being a chef, wants nothing more than to taste the succulent Jamie, but Chessene has been genetically enhanced by Dastari and she has a higher calling. She is working with the Sontarans to finalize the work on a Time Machine, and allows the fleet to enter the station, seemingly killing everyone on board.
Four regenerations later, the Doctor is harmlessly fishing with Peri when he realizes something is wrong. He receives a vision of his second incarnation being tortured to death. Peri suggests he see a Doctor so they travel to the science station Chimera, where Dastari is from. Arriving, they notice the stench of death in the air. Trying to determine what has happened, they encounter the only survivor, Jamie McCrimmon. The Doctor enters a trance and tries to telepathically connect to his former self to see where he was taken. A few minutes later, the Doctor, Peri and Jamie set off for Seville, Spain.
The Sontarans have persuaded the trio of Chessene, Dastari and Shockeye to Earth to finalize the Time Experiments. With the captured Doctor, they hope to harvest the symbiotic nuclei from within his cells, which is what makes time travel possible for the Timelords. Wisely, the Doctor refuses to help in the search. Dastari is saddened it's the Doctor he has to extract the nuclei from, but continues. With the augmentations he's given to Chessene, he hopes to put her 'among the gods'. The Doctor scoffs and says no matter how many augments she's received, she'll always have her true barbaric, animalistic tendencies.
As Dastari readies his equipment to search through the Doctor, Stike grows impatient. He tries to persuade the Doctor to give up the location of his nuclei, for the greater good of the Sontaran army. Realizing how high-strung the Sontaran is, the Doctor tries to enrage him, but fails. Stike turns his attention next to Dastari and threatens him to hurry up, but he's unable to convince him either. Dastari knows it's a bluff because he's needed alive, to perform the operation on the Doctor.
Arriving at the Spanish Hacienda, the Sixth Doctor sends Peri in to divert everyone from the basement while he and Jamie take a look around. Hearing Stike approach, the Doctor tricks him into thinking he can make the Time Machine operational immediately. Using Jamie as a threat, the Doctor is forced to prime the Time Machine, which he obediently does. Jamie and the Doctor are able to escape when Jamie stabs him with a knife. But the Sontarans are unable to test the primed Time Machine as Chessene betrays them and kills Varl and injures Stike with Coronic Acid. Stike manages to survive and hobbles to the Time Machine but finds out it's defective. He then remembers he ordered his Spaceship to self destruct thinking he was going to use the Time Machine to rejoin his fleet. He returns to stop the destruction, but is too late and killed in the blast.
In a change of plan, Chessene now instructs Dastari to create a consort for him using the Doctor as a template and infusing him with Shockeye's Androgum DNA. The operation is successful but when Shockeye awakes, he's enraged till the Second Doctor awakes and tantalizes him with descriptions of the local cuisine. Having been thwarted in his attempts to prepare and eat both Jamie and Peri, Shockeye is tempted and follows the Second Doctor to town. Over 80% Androgum now, the Doctor's thoughts are as primitive as the Shockeye's and can think of nothing better than to sate his stomach.
Chessene and Dastari set off to find the pair because if the Doctor isn't stabilized within the hour, his body will reject the Androgum DNA. But the Sixth Doctor, Peri and Jamie also set off to find the pair, hoping to keep the Second Doctor from transforming completely into an Androgum. The Doctor finally finds the Doctor after an hour has passed and his body quickly rejects the Androgum transmogrification. But Chessene also finds them and orders everyone back to the Hacienda at gunpoint. She ties up everyone else as Shockeye attempts once more to eat Jamie.
Working together, the Two Doctors manage to escape. The Sixth Doctor runs upstairs to rescue Jamie, but Shockeye finds him and cuts him. The Doctor runs away, leaving a trail of blood for Shockeye to follow. The Sixth Doctor eventually leads Shockeye into a trap and smothers him with a cyanide laced cloth, killing him. Dastari is revolted when he discovers Chessene's primal instincts kick back in when she falls to the ground, lapping up the Doctor's spilt blood. Realizing the Doctor was right all along, he finally sides with the Second Doctor. But Chessene kills him and tries to escape in the faux Time Machine. But the Doctor tricked Stike earlier and only primed the machine for a one time use. Having already been used, the machine blows up, killing Chessene. The Sixth Doctor is also happy to report, Shockey has met his just deserts.
Shockeye samples the local Earth cuisine.