(written from a Production point of view)
Archer, Reed, and Sato are threatened by a virus that mutates them into a primal lifeform.
On the Enterprise NX-01, it is late at night. Commander Trip Tucker visits Sub-commander T'Pol for a long-overdue massage session. To make up for missing the past two sessions, he brings some Georgia peaches which he got from Earth recently. T'Pol uses Vulcan techniques, but assures Tucker the risk of paralysis is minimal.
The session is cut short as Captain Archer calls T'Pol away. He is able to discover, from the Xindi's stolen database, the last planetary stop of the destroyed Xindi ship. These new Xindi seem to be evolved from primates. T'Pol notes they aren't necessarily the ones that attacked Earth, but Archer wants more information, ordering a course.
Upon arrival at the planet, Enterprise doesn't detect life signs, but does discover a metallic signature on the planet. Leaving Travis Mayweather in command, Archer leads an away team of Lieutenant Malcolm Reed, Hoshi Sato, and T'Pol, and eventually discovers a Xindi landing craft and some scorched corpses – not Xindi.
However, soon the away team is affected by a virus as they explore the surrounding area. T'Pol feels her temples bulge, and, upon seeing Reed again, she sees he has transformed into a primal-like creature. She heads back immediately to the landing craft, only to discover that Archer is now also infected. T'Pol immediately calls for a security team from Enterprise, but is soon attacked by Archer, now speaking in an alien language. She stuns him in a defensive maneuver, only to be attacked by Sato from her side, also transformed. T'Pol attempts to run away but falls and is rendered unconscious.
The troop of new mutants carries T'Pol's body using sticks and branches to a clearing and lays her down. As she wakes, the three seem to be having a discussion about her. T'Pol is tied up and, in a highly agitated state for a Vulcan, asks them to untie her. Archer does so, but seemingly under protest from Sato. Then, T'Pol convinces them to give her the universal translator and tries to get them to talk.
On the Enterprise, Doctor Phlox examines the new bio signs and is confident he sees a Vulcan one. The other three are not. Tucker wonders where their team is. Tucker wants to go down after them, but Phlox warns him, saying that T'Pol mentioned being "altered," and is guessing she meant literally. He wants more time to investigate, but Mayweather sees they're moving off, and Tucker decides he can't wait any longer. He orders the other shuttlepod prepared and environmental suits.
T'Pol makes some progress talking to them and trying to convince them to get back to the ship. However, she discovers they have a purpose: they are looking for Urquat. Sato and Reed are insistent on finding the rest of "their people," and they believe that T'Pol is lying to them. Archer hesitates. They obviously are intent on finding this Urquat, so T'Pol then tries allowing them to do so. On the way, she sees more of their primal behavior, as Reed climbs a tree incredibly quickly and finds food, immediately triggering a fight over the food among the three. Archer wrestles some food from Reed. Before he eats, he offers some of it to T'Pol, but she refuses. He then also allows Reed to have some.
Tucker takes down a rescue team of Corporal Chang and Private Palmer and they start searching. The mutants, with enhanced vision, have an advantage in observing the team from the foliage. Soon, Reed attacks Chang and knocks him out as Sato runs by Palmer, drawing him away. Tucker catches up with Chang, stuns Reed as he attacks again, then is attacked at close range by Archer. Archer bashes a crack in Tucker's helmet and intends to go again but T'Pol stops him, asking if he recognizes Tucker. Archer pauses to consider, but Palmer gets close and he runs away. T'Pol decides to stay with Archer and Sato, ordering Tucker to take Reed back to the ship.
A primal Reed is highly agitated in the decon chamber while Phlox observes him. Phlox confirms to Tucker they have a mutagenic virus and that T'Pol's Vulcan K-cells are apparently neutralizing the virus. He needs her active DNA as soon as possible to complete the cure.
However, two alien ships intercept Enterprise and declare them under quarantine. He demands they prepare to be boarded.
Tucker refuses to allow anyone on Enterprise, but the alien commander, Tret, says he detects the infected crewmember and that the virus must be eradicated, having been studied for 60 years without another option. Tucker is emphatic that there is no "outbreak" as Reed is in medical isolation. He invites the commander to the ship to discuss it, but promises a fight if he tries to board by force.
On the planet, Archer has a dream in which he discovers the great city of Urquat underground. Oddly, he sees himself (as a Human) approach him, jolting him awake. He happily tells Sato about the city, and they're both excited. T'Pol tries to state that his home is really Earth, but they both declare she's lying.
Tret comes aboard Enterprise and visits sickbay to observe Reed and inform Phlox and Tucker about the virus. He warns them that the virus is very dangerous and millions of his people had to be killed because of its rapid growth. An ancient race, called the Loque'eque, created the virus to perpetuate their race as they could no longer propagate. Tret's people intend to eliminate all infected victims as the virus spreads like wildfire and drives all who change into Loque'eque to find their home. Tret gets word from his ship that more infected are on the planet, and he orders a containment team together. Phlox says T'Pol is immune, and wants to work together with Tret, but Tret is insistent on examining them himself. He leaves, promising use of force if he is hindered from containing the outbreak. After, Phlox says he needs T'Pol's DNA within two hours, and Tucker gets an idea, remembering she bit into one of the peaches.
On the planet, the three close in on the city, however, they discover the lifeless ruins of Urquat.
Archer and Sato can't believe the city is gone, and dwell on it. T'Pol tries to say they can go to Enterprise to find out what happened to them, but Archer refuses. Then, he suggests it was T'Pol's race that destroyed them, and holds her by the neck as she denies it. Then, they are discovered by the aliens searching to destroy them, so they run. The three of them attack the aliens in caves and, in the ensuing melee, they are knocked out and the three escape to the surface at T'Pol's insistence. However, Archer manages to tear the suit of one of the aliens, thereby infecting him. His comrades promptly "torch" him when they find him. The three make it outside of the caves but are soon surrounded by the aliens. They force T'Pol away and prepare to torch the other two, but just then Tucker and the MACOs appear and stun the aliens. T'Pol makes a final plea to Archer to follow her to the shuttlepod, and he finally agrees.
As they approach the ship, Tucker orders Mayweather out of orbit, and they are soon chased by the alien containment force. Tucker tries to buy time for Phlox, but after being fired upon briefly, Tret hails them and orders them out of warp. Tucker pleads with him to allow them to find a cure. Tret dismisses it until he see the partially-cured Sato and Archer appear on the bridge. Tret has the ship scanned again and the aliens finally accept that a cure is possible, and break off the attack.
- "Captain's starlog, supplemental. We've given Phlox's serum to the captain of the containment vessel. With any luck, they'll be able to use it to prevent future outbreaks. As for Malcolm, Hoshi, and me, it may be a few days before we feel fully Human again."
Dr. Phlox wants to destroy the last of the mutagenic virus, thereby possibly eliminating the last vestiges of the Loque'eque. Archer doesn't want that to happen and orders the doctor to put the vial in stasis. Archer assumes that the unnamed aliens will destroy the last traces of the virus on the planet with their new cure. He reasons that soon the last trace of this civilization will be Dr. Phlox's sample.
"You sure this is safe? I mean, has anyone ever tried it on a Human before?"
"Not to my knowledge. The risk of paralysis is minimal."
- - Tucker and T'Pol, during a neuropressure session
"You're saying these alien bio-signs could be our people?"
"From what we've seen of the Expanse, it's a possibility we have to consider. The laws of biochemistry on this world may be just as unpredictable as the laws of physics."
- - Tucker and Phlox
"He didn't even recognize me."
"Don't be offended. In his current condition, I doubt he'd recognize any of us."
- - Tucker and Phlox, on the transformed Reed
"Your ship is in restricted space."
"Sorry. It wasn't very well marked."
- - Tret and Tucker
"Your vessel is under quarantine. Prepare to be boarded."
- - Tret, to Tucker
"Have you got anything for my stomach? Chef's food isn't sitting too well."
"Until your digestive tract is fully restored, you may want to avoid the mess hall."
"What do you suggest I eat?"
"You're welcome to some of the moth larvae I feed to my Pyrithian bat."
- - Malcolm and Phlox
- This episode saw the series' title change from Enterprise to Star Trek: Enterprise in the opening credits, though in the DVD, Blu-ray, and syndicated releases of the series, "Star Trek" appears in the title of all season three episodes.
- This episode was dedicated to the memory of Jerry Fleck, the show's first assistant director. This was the last episode on which he worked before dying in his sleep at the age of fifty-five.
- John Eaves notes in his blog that an earlier version of this episode's script called for a new Vulcan shuttle design, but was written out by the time it was filmed. He did, however, post sketches of the unseen shuttle, as illustrated by himself, on his website. 
- According to Trekweb, LeVar Burton went to the producers and told them he was "ashamed" that he had directed this episode.
- Ten years after this episode aired, Brannon Braga called "Extinction" "one of the singularly most embarrassing episodes of Star Trek I've ever been involved with." ("In a Time of War, Part Three", ENT Season 3 Blu-ray special features)
- This episode shares similar plot elements to TNG: "Identity Crisis", where Geordi La Forge is transformed into another species in an extremely short timespan, as well as TNG: "Genesis".
- Two flame throwers used in this episode were auctioned off in the It's A Wrap! sale and auction.  
- Ensign Mayweather enjoys a brief period as ranking bridge officer on board Enterprise when all his seniors are off ship in the fourth act.
- Several costumes and props from this episode were sold off on the It's A Wrap! sale and auction on eBay, including the boots of Brian J. Williams. 
Links and references
- Scott Bakula as Captain Jonathan Archer
- John Billingsley as Doctor Phlox
- Jolene Blalock as Sub-Commander T'Pol
- Dominic Keating as Lieutenant Malcolm Reed
- Anthony Montgomery as Ensign Travis Mayweather
- Linda Park as Ensign Hoshi Sato
- Connor Trinneer as Commander Charles "Trip" Tucker III
- Craig Baxley, Jr. as Decon Agent #2
- Kiante Elam as a Xindi-Arboreal pilot
- Glen Hambly as a operations division ensign
- Jimmy Ortega as Decon Agent #3
- Keith Shindoll as Decon Agent #4
- Diamond Farnsworth as stunt double for Scott Bakula
- Dan McCann as stunt double for Scott Bakula
- Gail Monian as stunt double for Linda Park
- Marty Murray as stunt double for Dominic Keating
- Boni Yanagisawa as stunt double for Jolene Blalock
2090s; ability; antivirus; biochemistry; bio-hazard protocol; blood; century; Chef; chromophyllic plant species; command center; contagion; Delphic Expanse; digestive tract; DNA; Earth; ecosystem; equatorial islands; EV suit; extinction; fountain; garden; Georgia; humanoid; immunity; K-cell; land mass; larva; Loque'eque; Loque'eque homeworld; Loque'eque language; moth; mutagenic virus; neural node; oxidation; peach; Pyrithian bat; quarantine; race (species); reproduction; serum; Shuttlepod 1; Shuttlepod 2; sole; stomach; transporter; Tret's containment vessel; Tret's species; tropics; Urquat; Urquat citizens; Vulcan; Xindi-Arboreal; Xindi-Arboreal landing craft; Xindi database
- "Extinction" at StarTrek.com, the official Star Trek website
- "Extinction" at Memory Beta, the wiki for licensed Star Trek works
- "Extinction" at Wikipedia
- Design sketches for the ships and locations seen in the episode at Eavesdropping with Johnny
| Previous episode:|
| Star Trek: Enterprise|
| Next episode:|