Tom Paris is in an experimental shuttlecraft, attempting to break the warp 10 barrier. He brings the Class 2 shuttle up to warp 9.95, when the nacelles are suddenly ripped from the shuttle and it seemingly explodes. Paris appears, sitting on the holodeck floor, as if nothing happened; it was all a holographic simulation. Harry Kim looks despondent, and B’Elanna Torres responds matter-of-factly, “You’re dead.“
The trio go to the mess hall to consider how to fix the problem. Neelix offers to help, but they don’t believe he can contribute anything to the discussion. Paris inquires if he knows anything concerning quantum warp theory and multispectral subspace engine design. Insulted, Neelix informs them that serving for two years as an engineer’s assistant aboard a Trabalian freighter makes him well versed in warp theory and demands to know what they’re up to. They finally fill him in: after months of experiments, Paris, Torres and Kim believe they have found a way to cross the transwarp threshold using a new form of dilithium they discovered in a survey of an asteroid field that remains stable at higher warp frequencies. Achieving warp 10 would allow a person to be in every point in the universe, simultaneously.
Kim notes that getting home could be as quick as the push of a button. A problem occurs when the ship reaches warp 9.95, when microfractures appear and tear the nacelles from the ship. Neelix recalls an anecdote from his past when his ship was traveling through a dark matter nebula. Kim is initially dismissive, as this is a totally different phenomenon, but Paris realizes that it is actually the shuttle being ripped from the nacelles, not the other way around. While Kim confirms the tritanium alloy hull could depolarize at that speed, Paris continues, saying that could create a velocity differential, the fuselage traveling faster than the nacelles. As Kim infers, they could fix the problem by installing a depolarization field around the fuselage. Paris refers to the confused Neelix as a genius and runs out to the holodeck with Torres and Kim.
In the briefing room, the senior staff watch the holodeck simulation on the computer monitor and grin as Paris successfully brings the shuttle to warp 10 and crosses the transwarp threshold. Captain Janeway gives Paris the opportunity to start a manned test flight in a real shuttlecraft. She says he has the opportunity to join such great names as Orville Wright, Neil Armstrong, and Zefram Cochrane. Everyone is excited because, if this works, then it would mean much more than just getting USS Voyager home; it could begin a whole new era of exploration for Starfleet.
Janeway enters Paris’ quarters that night, with news that The Doctor discovered an enzymatic imbalance in his cerebellum that appeared during the holodeck simulation; the subspace stresses could kill him from a brain hemorrhage, although the chance is only two percent. Not wanting to risk this chance, Janeway plans to assign Ensign Kim to the flight. Paris begs her to reconsider, stating that people have always said he was going to do something special someday, and that this is it. Janeway agrees to it, and the next morning Paris boards the shuttlecraft, now named Cochrane, and launches it. The shuttle kicks into warp, followed closely by Voyager. After running a few scans on the Cochrane‘s warp field at warp 9.7, Torres clears Paris for transwarp. Voyager increases to warp 9.975, its maximum velocity, for as long as it can but, as Paris quickly surpasses that speed, Voyager must slow and switch to long-range sensors to track him. As the crew waits in anxiety, Paris goes faster and faster until, finally, sensors record warp 10. Then, the Cochrane vanishes.
A search fails to turn up the Cochrane, but then it reappears. Lieutenant Paris is still on board, but unconscious, with weak life signs. In sickbay, The Doctor scans him and observes that Paris is merely sleeping. The Doctor abruptly wakes Paris and he recounts his transwarp flight to Captain Janeway. He says he was staring at the velocity indicator (which read warp 10) and then, suddenly, he noticed he was watching himself. He could see the outside of the shuttle, Voyager, the inside of the ship, and the sickbay. For a moment, he was everywhere, with the Kazon, the Klingons, on Earth, and he even saw other galaxies. He says it wasn’t like anything he has ever experienced. According to Paris, he only returned because he noticed that the crew was looking for him. Torres bursts into the room and says that the on-board shuttle sensors confirm he flew warp 10, making Paris the first Human to break the transwarp barrier. Paris asks Torres to download the shuttle’s data core while The Doctor runs further tests on him.
Kim downloads the shuttle’s data into the engineering computer core – over five billion gigaquads of information – including detailed information on “literally every cubic centimeter” of the sector. Janeway orders the data sent to stellar cartography for analysis and the creation of a star chart.
After being released from sickbay, Paris is in the mess hall with Torres, where they are planning another flight to replicate the results of his first test. He begins to say the shuttle’s memory core should be increased when, all of a sudden, Paris feels ill. First, he has a sip of Neelix‘ new Paris Delight blend of coffee and says it’s awful, though Torres says it smells all right. Then he experiences a stomach ache, and then collapses to the floor writhing in pain. Torres asks the transporter room to beam him to sickbay but they respond by saying that they can’t lock onto him; his pattern keeps changing. Torres calls for medical assistance and tells Paris to hold on.
The Doctor examines Paris in sickbay and says he had an allergic reaction to, of all things, the water in Neelix’s coffee. In fact, Paris’ entire body is mutating and his lungs are no longer processing oxygen. The Doctor replaces the atmosphere in the surgical bay with 80% nitrogen and 20% acidichloride. Paris can now breathe but a bigger problem has also developed; he is suffering from cellular degradation and is consequently dying.
The Doctor and Kes begin using radiation to try to stop it, with little success. Paris becomes delirious, asking for a huge funeral, saying he doesn’t trust anyone that doesn’t cry (like Torres) and remembering his childhood, when he used to cry in his room. He tells The Doctor that he lost his virginity at seventeen, in his room, which The Doctor says he will note in Paris’ medical file. Paris exclaims he wants a pizza with pepperoni and Kavarian olives. He wants a kiss from Kes but she can’t grant him that wish, because of the atmosphere in the surgical bay. Before he dies, he makes a last request; to tell his father that he did it. He tries to form another sentence but falls unconscious. The Doctor uses a neural stimulator to attempt to revive him but fails. The Doctor announces Paris’ time of death and plans to perform an autopsy in the morning. Kes kisses Paris’ apparently lifeless body before she leaves sickbay.
That night, as The Doctor is working in his office, he hears a strange rattling in the other room. Uncovering Paris’ body, he discovers him alive and well. Paris looks at his hand, then reaches up and pulls out a clump of his hair and demands to know what’s happening to him. The Doctor scans him and finds something peculiar; Paris now has two hearts.
Crewman Michael Jonas, in his quarters, covertly sends data on the warp 10 shuttle flight to Rettik, his contact among the Kazon. Although Rettik doesn’t believe it, Jonas sends him the entire file in an attempt to prove his worth to the Kazon-Nistrim.
The Doctor briefs Janeway on Paris’ condition. He cautions her that not just Paris’ body but also his personality is affected, he keeps switching from his original personality to one that seems deranged.
Janeway walks into sickbay to see a mutated Tom Paris lying on the biobed behind an isolation field. Paris says he feels “like a lab experiment that went wrong.” She offers to help, but Paris’ personality switches and he becomes furious. He says he is glad that he’s changing and thinks that whatever he will become will be better than what he ever was. He demands that they stop trying to reverse his mutation. He doesn’t believe anyone likes him and, in fact, he suspects they’re jealous that he broke the warp 10 barrier. Janeway walks away and concedes there’s nothing she can do. Paris’ personality switches back again and he pleads with Janeway to help him, but then he lashes out, hitting the isolation field in front of him. He begins to tell Janeway how small and insignificant she is, when he starts to choke. Paris then vomits out his tongue and smiles.
Later, Kes discovers that Paris’ rate of genetic mutation has accelerated by another 12 percent. The Doctor and Kes must hurry to save the last fragment of Paris’ original Human DNA. Paris pleads to be let off the ship. They refuse.
After further analysis, The Doctor derives a treatment. He plans to revert Paris’ body back to its original genetic coding by destroying the mutated DNA using anti-proton radiation from the warp core. They have to have the system set up in an hour if they hope to save him.
Paris has mutated even further. He is in a restraint situated next to the warp core in main engineering. The core shuts down to give Paris a two-second burst of anti-protons, but it’s not working. Paris begins to struggle out of the restraints. The Doctor asks Torres to start a five-second burst of anti-proton radiation, when a commotion is heard in the background. Paris bursts out of his restraints. Phaser fire erupts in engineering, then the engineering screen where The Doctor was observing the procedure goes dark. The lights in the room start to flicker; Paris ruptured the port plasma conduit on his way out of engineering, causing power failures all over the ship. Tuvok announces a level 3 security alert over the comm system.
Janeway is on Deck 6 outside a turbolift when Paris attacks her from behind.
She manages to fire her phaser, triggering the internal sensors, but they are malfunctioning due to the power failure. Consequently, the bridge can’t localize her exact position. However, Kim is able to report that the captain is between sections 21 and 27 Alpha.
Chakotay orders Tuvok’s security personnel to that section of the ship, but it is too late. Paris takes Janeway to shuttlebay two and launches the Cochrane. The shuttlecraft immediately speeds to warp. Just then, main power on Voyager is restored and the ship heads after the Cochrane in pursuit. Voyager capably follows the shuttle until it reaches warp 9.975. Chakotay pushes the ship’s acceleration even more, but slows back when the main computer issues a warning that Voyager‘s structural integrity will fail in 45 seconds. Paris and Janeway meanwhile cross the transwarp barrier, becoming no longer visible from Voyager.
After summoning Tuvok and Chakotay to sickbay, The Doctor observes that what happened to Lieutenant Paris was an accelerated form of natural Human evolution that would otherwise have taken millions of years. It is possible that Paris shows an advanced form of Human life. The Doctor comments that the lifeform isn’t very attractive. He is still confident that the anti-proton radiation will work to revert Janeway and Paris back to their original Human DNA.
Kim reports, from the bridge, that ship’s sensors have located the Cochrane on a remote planet in one of the jungles near the equator. Chakotay and Tuvok beam down with an away team to investigate. On the planet, they see two amphibian-like beings. Chakotay checks them with his tricorder and finds traces of Human DNA. The two have apparently reproduced, as there are several juveniles of the same species nearby. Chakotay stuns the two adult creatures with his phaser and brings them back on the ship. Chakotay has no idea which creature is Janeway. However, Tuvok notes the obvious deduction that Janeway must be the female.
“First officer’s log, supplemental. We’ve transported the captain and Mr. Paris back to sickbay. As for their… offspring, I’ve decided to leave them in their new habitat.“
Paris and Janeway are reverted back to their Human selves using The Doctor’s anti-proton treatments. Afterwards, Paris is extremely embarrassed about having mated with the captain, though he says he hardly remembers the whole event. Janeway accepts his apology, but admits that she might have also been active in the mating process; she may even have been the one who initiated it. Janeway puts Paris in for a commendation for his achievement. “Regardless of the outcome, you did make the first transwarp flight.” Paris admits he has a few more barriers to break to build his self-esteem, but Janeway believes he will eventually overcome them.