While on their way to Azati Prime, the Enterprise discovers a Xindi ship and Archer sends an away team to find out about their technology. When they arrive, they find that the crew is dead and the life support is down. They explore the ship in EV suits and find a room with working life support that's full of eggs, where Archer is sprayed with liquid from the ceiling. Phlox finds out it's a neurotoxin but that the captain is probably fine. Back on the Xindi ship, the crew finds out that the life support is in danger of failing, and if it fails, the eggs will die.
Archer wants to save the Xindi babies by powering up the old ship, but Trip is against this, feeling that the longer they stay, the more likely it is for them to be spotted by Xindi. Over two days, they try various methods of powering it up, but none of them work. Archer, who is getting increasingly more frustrated, has an idea: send antimatter to the planet the ship is orbiting. However, T'Pol is opposed to it.
On the derelict Xindi ship, T'Pol explains that the reason she's against the idea is because Enterprise is already running low on antimatter, but Archer insists on sending some to the planet anyway and has T'Pol relieved of duty and confined to quarters.
While discussing Xindi ship tactics with Reed, Hayes discovers a flaw in their shields, which impresses Reed. Meanwhile Trip convinces Chang to let him visit T'Pol under the pretense of a neural pressure session. T'Pol convinces Trip that Archer is behaving irrationally and putting the mission in danger, but Trip doesn't want to confront him for fear of also being relieved and confined to quarters.
Archer puts Hayes in command, posts MACOs all over the ship, orders Hoshi to send a distress call, and goes to the shuttlebay to begin loading a shuttle with antimatter. T'Pol and Phlox try to convince him to go to sickbay for a an examination, and he refuses, but Phlox manages to scan him. Phlox finds nothing wrong, but Trip is unconvinced and begins planning a mutiny.
Reed frees T'Pol from her quarters by force and they take over the armory and steal some phase pistols. Then, Trip and a random crew member transport to the surface to confront Archer, while Reed, T'Pol, and several others try to access the bridge. On the bridge, Hayes discovers that Chang is incapacitated and T'Pol has escaped, and moments later, the mutineers arrive. A fight breaks out, which leads to the MACOs being confined to quarters.
On the Xindi ship, Trip finds Archer with the newly-hatched baby Xindi and has to stun him to get him to return to Enterprise. Phlox scans him again in sickbay and finds out that the only reason he wanted to save them was because that neurotoxin from before made him subconsciously think he was their dad. Then, he reverses the effect and they continue to Azati Prime.
Tropes in this episode include:
- Apologetic Attacker: Malcolm says, "Sorry" right before stunning the MACO in the armory.
- Bizarre Alien Biology: Phlox learns a lot about the Insectoids from performing an autopsy, specifically that they reproduce asexually and live about twelve years.
- Call-Back: The regulation that Phlox threatens to use on Archer is practically the same one that McCoy tries to use on Decker in "The Doomsday Machine."
- Chekhov's Gun: Archer's increasingly illogical behavior is explained by the stuff he gets sprayed with early on, causing a reverse-imprinting.
- Chekhov's Lecture: Hayes discovers that Insectoid ships are weakest at their impulse manifolds. During a later firefight with an Insectoid ship, Malcolm orders an attack targeting the impulse manifolds, destroying the ship.
- Conforming OOC Moment: Even T'Pol, who is usually very by-the-book, joins in on the mutiny.
- Death of a Child: An early attempt to reactivate the Xindi ship's life-support system destroys an egg, causing the infant inside to be prematurely hatched. Archer desperately has it beamed to sickbay, but Phlox is unable to save it.
- Easily Forgiven: Everyone agrees to put the events of this episode behind them.
- Foreshadowing: The Insectoid shuttle that the crew salvages will be put to use in the next episode.
- Holding Your Shoulder Means Injury: Trip does this when telling the MACO guarding T'Pol's quarters that he needs to see her for neuropressure. It fails, so Phlox uses the off-button hypospray on him instead.
- Heroic Sacrifice: The Insectoid crew died when they transferred their remaining life support to the hatchery.
- A House Divided: Unfortunately Enterprise now has two factions that can take sides — Archer's fellow officers, who know he's Not Himself but now have the confidence to act against him, and the MACOs who are trained to obey their superior officer without questioning him.
- Imprinting: Inverted; the goo made Archer subconsciously think he was the Xindi babies' father.
- Mexican Standoff: When the Starfleeters storm The Bridge and confront the MACOs.
- Screw the Rules, I'm Doing What's Right!: When Trip decides to start The Mutiny."I think it's time we throw the rulebook out the window."
- Skewed Priorities: How pretty much everyone sees Archer's desire to save the hatchery instead of proceeding to Azati Prime. While Trip initially justifies this by saying they could use an extra day or two to study the Insectoid ship, as they'll likely run into more of them soon enough, he realizes something has to be done when Archer orders them to use more and more resources to save the hatchlings.
- That's an Order!: Archer orders T'Pol to oversee the antimatter transfer from Enterprise to the Insectoid ship. When she refuses, he orders Hayes to confine her to quarters.
- That's Gotta Hurt: When Malcolm stuns one of the MACOs guarding the armory:Trip: That's gonna leave a bruise.
- The Mutiny: Trip and T'Pol are left with no choice but to start one.
- What Measure Is a Non-Human?: When Trip suggests torching the hatchery, Archer asks him if he'd torch a Xindi-Primate nursery.
- Writers Cannot Do Math: Archer says that his great-grandfather fought in North Africa during the Eugenics Wars, which took place during the 1990s. Even if the Archers waited to have children, this would still be about a generation off. However, later Star Trek series would justify this by pushing the wars back a few decades.
- You Are in Command Now: After relieving both T'Pol and Malcolm, Archer puts Major Hayes in command.
