Star Wreck: In the Pirkinning picks up where the previous movie, Star Wreck V: Lost Contact, left off. Captain James B. Pirk (Samuli Torssonen) is stranded with his crew, Commander Dwarf (Timo Vuorensola) and Commander Info (Antti Satama), on turn-of-the-millennium Earth. Life is not good. Dwarf works in a small-time hot-dog stand, and Pirk is stuffing himself with hamburgers, while trying to pick up girls. Info's whereabouts are unknown.
During their stay on Earth the timeline is wrecked beyond repair, so Pirk decides to take fate into his own hands. Pirk locates the space ship of the Vulgars (a parody of Star Trek's Vulcans), whose first contact mission was corrupted by a hedonistic rock star who took them into his charge, which was sold to Russia, and incites the Russians at the Chanistanya nuclear research facility to a revolution and to build a new ship, the C.P.P. Potkustartti (translated as Kickstart). With the help of the Russians and their President Ulyanov (Kari Väänänen), the P-Fleet is born again, as Pirk's empire. Earth falls quickly under Pirk's rule, but the relatively primitive technology of the new P-Fleet's ships prevent them from expanding the new empire onto other habitable planets.
By Sergey Fukov's freak encounter with a maggot hole (a parody of a sci-fi staple, the worm hole), Pirk is given a new idea of conquest. Pirk's hunger for power and profound lack of reason drives him through the maggot hole, behind which he finds a parallel universe. In this universe, history has taken a completely different path, leading to Babylon 5-like technology. Hell-bent on conquest, Pirk unwittingly reveals his plans of invading the parallel universe Earth to the commanding officer of the Babel 13 (resembling the Babylon 5 space station), by which he commits himself into a mortal battle with Babel 13's forces.
The tide of the battle turns with the intervention of relief forces lead by the Excavator, commanded by Festerbester. After a bitter fight, Pirk must flee back into his own universe where he will have his final brush with fate, being once again stranded on Earth, without a ship, during an ice age. There is some controversy over whether they are, as Info suggests, stranded 11,000 years in the past, or if they are actually far in the future beyond hope (as suggested by the appearance of space debris when the camera zooms out from Earth just before the credits).