Our story starts off with the Second Doctor and Jamie being sent around time and space, on a mission from the Time Lords. They look far older than they did in "The War Games", which is never explained or mentioned in any way (although the "Season 6B" theory has since made its way into official BBC policy and Terrance Dicks' novels).This time, they head off to a space station where a doctor named Dastari is making some incredible leaps forward in time travel science that the Time Lords are objecting to in some fashion. Dastari objects to the Time Lords being their Jerk Ass selves and gets into an argument with the Doctor, who isn't exactly thrilled to be there either. But since the Time Lords can always claim that they had nothing to do with him, they're using him as the perfect scapegoat while threatening Dastari. Meanwhile, Sontarans invade the space station — and the Doctor orders Jamie to run away as they point their guns at the Doctor...Cut over to the Sixth Doctor, who is having a nice fishing holiday with Peri. The Doctor suggests heading off to the Eye of Orion... and then collapses in pain and agony. We see a montage of Jamie back on the station seeing the Second Doctor dying miserably. The Sixth Doctor reawakens, having just seen a mental image of his second self being put to death. Realizing this can't be possible as he's still alive in the future, he decides to go figure out what the hell just happened anyway — deciding to consult Dastari on what is going on.The Doctor and Peri bumble around the space station until they finally stumble onto an incoherent Jamie. He reveals that the Second Doctor was just killed. The Sixth Doctor figures this has to be a lie, as time hasn't wiped him out yet, and fiddles around the station until he figures out that it was all just an illusion that took the episode about 20 minutes to work past. This means, Sixth figures, that his Second self is being held captive somewhere. He puts himself into a trance to try and find him mentally. Waking up some time later, the Doctor comes to the realization that Two is being held in Seville, Spain, by the combined forces of the Sontarans and Dastari.However, Dastari is more of an unwilling companion, as most of the planning is being done by his lady-friend Chessene and an "Androgum" called Shockeye... a stereotypical alien-Scotsman who really likes to eat meat. (This makes just slightly more sense when you know that the author intended the story to be a pro-vegetarianism allegory.)The Sixth Doctor, wearing slightly-more-tasteful vest instead of that horrible coat for the occasion, lands the TARDIS outside Seville. They're approached by a vacationing couple: Oscar Botcherby and Anita. Oscar is managing a restaurant in the city, but is currently catching moths. As it turns out, Oscar also happened to see what he thought was a plane crash earlier on a mansion — but it just so happened to be the Sontarans' spaceship landing to meet up with Dastari. Seeing the TARDIS, he mistakes the heroes for British policemen. Sixth is then escorted to said mansion, which he scouts out for a little while, having told everyone else to wait just out of sight.Dastari and the Second Doctor have a nice little talk, where Dastari reveals that his lady-friend Chessene is actually an evolved Androgum. This information pisses off the Doctor to no end, and it only makes him angrier to find out that Dastari now wants to give the Doctor's Time Lord DNA to Chessene as well to make her even more awesome... completely ignoring the fact that the base of Chessene's enhanced DNA, Shockeye, is a ginger backstabbing alien bastard with a lust for power and hunger for flesh. Seriously.Jamie and Sixth go down to the basement of the building and find a mini-TARDIS under construction. The Doctor talks technobabble to Jamie about how they won't be able to complete it, and Jamie just looks at the Doctor like he's got a Sontaran behind him. Which he does. Whoops. Meanwhile, Peri decides to wander into the mansion on her own, posing as a lost American student... which doesn't work either, as Shockeye decides she'll make a lovely lunch.Jamie and the Sixth Doctor escape the Sontaran without much trouble, but one part of the technobabble that the Sontarans/Dastari need to complete the mini-TARDIS is given to them. They also find the Second Doctor tied up in a wheelchair, finally awake again. However, before they can escape with the Sixth's younger self, Shockeye comes back into the mansion, Peri over his shoulder.The subplot with the mini-TARDIS and the Sontarans is eventually resolved in a plan that doesn't entirely make sense to anyone but the Sixth Doctor, who just grins the way he does. Chessene also decides to try and kill off the Sontarans before they can take the mini-TARDIS for themselves, intending to give it to her own Androgum people. Jamie, meanwhile, is being "tenderized" by Shockeye for the next meal, Peri having escaped only to be recaptured by the Sontarans and used as part of the mini-TARDIS subplot.Dastari, for his part, has converted the Second Doctor into a half-Androgum with ginger eyebrows, to make him a consort for Chessene. Shockeye is miffed at this, as Dastari used his blood to do so, until the Second Doctor decides that he wants to go eat a lot of food and knows where to go. Shockeye, being an Androgum, goes happily along with the Doctor. The two of them indulge in their Horror Hunger in matching top hats and have a massive feast at the restaurant run by Oscar. When Oscar rather politely presents the bill, he's killed by Shockeye. The Sixth Doctor, Jamie and Peri (who somehow got freed from their individual subplots for a time and pursued the pair) arrive just in time to see Oscar die, Anita cry, and the Second Doctor revert to normal... because apparently an hour has passed and his body rejected the conversion or something.The Second Doctor, Peri and Jamie run back to the mansion to destroy the mini-TARDIS once and for all while the Sixth Doctor pursues Shockeye. Chessene decides to elaborately lick some blood from Six' new stab wound from her fingers. Stumbling across Oscar's moth-catching equipment, Sixth uses the cyanide-soaked cotton balls stored in a jar to kill Shockeye and then delivers a Bond One-Liner: Shockeye got his just... desserts. The Sixth Doctor then finally arrives back at the mansion just in time to be captured alongside his previous incarnation and their companions by Chessene and Dastari. Chessene begins to revert back to her Androgum heritage, which disgusts Dastari, who decides to free the Doctors and companions. Chessene shoots Dastari and flees in the mini-TARDIS, which then explodes and kills her before it really goes anywhere because of the sabotage that the Sixth Doctor did to it not long ago.The entire plot resolved in a really round-about way, the Sixth Doctor and Second Doctor exchange banter before Second summons up his own TARDIS using a Stattenheim remote control. Six expresses a little jealousy over the remote as Two and Jamie leave off on more adventures we'll never see, presumably losing the remote again along the way. Six and Peri leave the mansion, and both decide to vow to become vegetarians thanks to their horrid experiences with the Androgums.
As an interesting aside, the Doctor will remain a vegetarian until the Ninth Doctor orders a steak in "Boom Town" (he also almost eats a roast in "The Empty Child"). Russell T. Davies deliberately wrote his Ninth Doctor as a meat-eater again, to signify Character Development and the Doctor's change in attitude compared to the John Nathan-Turner days.