At the conference hall, Soval notes that people have been swarming around the Vulcan Compound, while Thoris reports similar activities around the Andorian embassy. Meanwhile, in Archer's ready room, Samuels orders him to attack the array, but he can't because two of his people are being held hostage there. Samuels insists, but Archer decides to instead sneak a ship over to Paxton's facility.
On Mars, Paxton is holding Trip and T'Pol hostage, and he shows them their daughter, revealing that she was created with her parents' DNA samples. He tells Trip to help him refine his targeting system for the array, and when Trip says no, Paxton has Josiah aim a weapon at T'Pol's head.
Malcolm meets up with Harris in an alley in San Francisco and asks him for information about Mars. Harris reveals that the sensors on Mars have been glitching out due to the atmosphere, which could allow a ship to go there. The two men then part ways, noting that they'll probably never see each other again if the Coalition of Planets arises. Meanwhile, Archer, Malcolm, and Travis plan to send the shuttle to Mars, while disguising it in the path of the comet, assuring a dubious Samuels that destroying the facility is Plan B.
At Orpheus, Paxton tells T'Pol, who is rocking the baby, that the baby will never be fully Vulcan or human and is a threat to humanity, but T'Pol counters him, saying humanity has always been changing, as have other species. She notices his hands shaking and scans him, then says that she won't let him hurt her kid, but he cryptically says that he wouldn't have to.
Travis visits Gannet in the brig. There, Brooks tells Travis that he is actually working for Starfleet Intelligence and not Terra Prime. Archer leaves Hoshi in charge, while Paxton rants to Trip about the Vulcans not helping the humans during World War III. He calls Trip and T'Pol's daughter a "half-human thing", causing Trip to punch Paxton in the face and sabotage the targeting system. Meanwhile, Archer, Malcolm, Travis, and Phlox head out in the shuttle.
Paxton catches Trip's sabotaging and demands that he fix the targeting system. When Trip refuses, Paxton claims that Trip is "eager for a bloodbath" and orders him to be put in a detention centre. Meanwhile, T'Pol spends some time with the baby.
The shuttlepod crash-lands on Mars and they head for Orpheus, while Trip makes a tool which he uses to break out of his cell. Josiah brings T'Pol into Paxton's office to talk, where she reveals that his shaky hand is due to a syndrome that is treated with Rigellian therapy, thus making Paxton a hypocrite. She also reveals that the baby has a fever and elevated white blood cell count, but Paxton claims that the baby is doomed to die because her "two halves are at war".
Samuels arrives on the Enterprise's bridge, believing that Archer, Malcolm, et al have failed. He tries ordering Hoshi to destroy the array, but she refuses to do so unless the worst comes to the absolute worst. Archer, Malcolm, Phlox, and Travis finally reach Orpheus and team up with Trip. They contact Enterprise, then Trip attempts to shut down the array, but is caught by Greaves, leading to a firefight, during which the window breaks. Eventually, the beam is fired, but it lands harmlessly in the ocean.
Paxton is put in custody, but there is a new problem: the baby's (now named Elizabeth) condition has become life-threatening and Phlox doesn't know how to treat her. He reveals that it was because the doctors' creation of her was imperfect. Malcolm and Travis, meanwhile, discover that Shuttlepod 1 crashed because it was sabotaged, and when they discover it was Ensign Masaro, he kills himself.
Samuels says to the alien delegates that Terra Prime was an example of humans at their worst, but that shouldn't affect their perception of humans in general. He honours the Enterprise crew, and Archer does a rousing speech, prompting everybody to clap.
Gannet is released and taken back to Earth by Travis, but unfortunately, Elizabeth dies, leaving Trip and Phlox in tears and T'Pol sitting dolefully on her bed.
Tropes in this episode include:
- Bittersweet Ending: Quite bittersweet. On the one hand, the conference moves forward, a significant step to what will become the Federation. On the other, Trip and T'Pol must endure the worst pain imaginable: a parent losing their child. On the OTHER other hand, Elizabeth died not because humans and Vulcans are incompatible, but because the method in which she was created made her an imperfect hybrid. So future human/Vulcan babies should be fine.
- Broken Pedestal: Paxton seems to have this view of Archer. Terra Prime gained newfound support as a result of the Xindi threat, and Paxton expresses actual disappointment over how "the man who delivered us from the Xindi" is opposing his efforts instead of joining them.
- Butt-Monkey: Kelby was originally going to be The Mole who commits suicide, but the writers decided he had suffered enough and invented a new character Ensign Masaro. Kelby's just a brief Red Herring suspect.
- Call-Back: Travis mentions that he has experience with comets. Didn't he break his leg on the last one? Probably best that he didn't mention that detail to Samuels.
- Call-Forward: Trip says that Phlox found a flaw in the method used to create Elizabeth, and determined that there's no reason why a human and Vulcan couldn't reproduce. In a hundred years, there will be a human-Vulcan hybrid who will become a Starfleet legend. His name is Spock.
- Character Check: The scene where Archer leaves Hoshi in command alludes to the close platonic relationship they had at the beginning of the series. This sets up Hoshi displaying a little Character Development while in command.Archer: I remember when you used to jump every time the engines hiccuped.Hoshi: I still do. I'm just better at hiding it.
- Continuity Nod:
- Phlox provides Malcolm with a vomit bag on the shuttlepod in response to his motion sickness. He wastes little time in using it off-screen.
- In "E Squared," Phlox is told that he would eventually discover a means of successfully combining human and Vulcan genomes. He manages to do so here.
- Dead Guy Junior: Trip names the baby "Elizabeth," for his sister who was killed in the Xindi attack.
- Death of a Child: Elizabeth's fever and elevated white blood cells that resulted from her imperfect cloning end up killing her.
- Die Hard on Mars: Couldn't let the final season end without one last episode of this.
- Driven to Suicide: Masaro phasers himself in the head right in front of Archer.Masaro: (with a phase pistol) Captain.
Archer: You don't want to do this.
Masaro: I have to.
Archer: Give me the phase pistol. That's an order.
Masaro: I can't, sir.
Archer: Ensign.
Masaro: I wanted you to know...I'm sorry. I believed in what we were doing. Tell my parents...I'm sorry. I never wanted anyone to get hurt.
Archer: Ensign!
Masaro: (shoots himself) - Evil Cannot Comprehend Good: Paxton is surprised that T'Pol doesn't see baby Elizabeth as a threat to the Vulcan species' survival, just as he sees her as one to humanity. T'Pol points out that all species are constantly changing, but Paxton remains unmoved, insisting that change "in this case" means extinction.
- Foregone Conclusion: Spock's very existence in the franchise is the biggest piece of evidence against the hypothesis that the baby died because of incompatible chromosomes.
- Grew a Spine: While in command of Enterprise, Hoshi demonstrates this by putting Minister Samuels in his place when he tries to order her around.
- Half-Human Hybrid: This is the second and last appearance of the Vulcan/human hybrid baby, who is named Elizabeth in the episode.
- Hybrids Are a Crapshoot: Zigzagged with Elizabeth. Throughout the episodes, the baby has a fever and high white blood cell count which ultimately kills her, and other characters wonder if it's because humans and Vulcans have incompatible chromosomes. As it turns out, however, the baby was just created imperfectly; humans and Vulcans are indeed capable of safely interbreeding.
- Hypocrite: As T'Pol points out, Paxton has a degenerative disease and is only being kept alive thanks to alien medicine. Had he been alive during Colonel Green's reign, he'd have been killed too. She also doesn't buy his attempt to justify it.Paxton: I'm not the first significant leader to fail to measure up to his own ideals.
T'Pol: You're not significant! - "It" Is Dehumanizing: Paxton keeps calling the child "it." Trip calls him on it.
- Manly Tears: Trip is clearly devastated by Elizabeth's death, as is Phlox.
- The Mole: Someone whom we've never seen or heard of before. Also, Travis' girlfriend Gannet, who's actually with Starfleet Intelligence.
- New Era Speech: Continued from last episode.Paxton: We do not seek war, but if the aliens do not leave, and force us to fight, I make this solemn promise to all of the sons and daughters of Earth. Our future will be secure because humanity will prevail.
- Not So Stoic: You can see the Suppressed Rage in T'Pol during her confrontation with Paxton.
- Only Bad Guys Call Their Lawyers: When Gannet is accused of being The Mole for Terra Prime and her alibi falls apart, she clams up and demands a lawyer, to which the Enterprise crew throw up their hands in dismay — they obviously think she's stalling for time. It turns out that while she is a mole, she's actually working for Starfleet Intelligence, not Terra Prime.
- O.O.C. Is Serious Business: One can tell that baby Elizabeth is dead when the normally chipper Phlox is crying and T'Pol, who, as a Vulcan, usually has flawless posture, is slouching.
- Remember the New Guy?: When the mole is uncovered in the last five minutes, the episode tries to establish that Archer and the crew are already familiar with him.
- Rousing Speech: After an entire show of mediocre speeches, including the infamous "gazelle speech," Archer closes with his best speech."Up until about a hundred years ago, there was one question that burned in every Human, that made us study the stars and dream of traveling to them. Are we alone? Our generation is privileged to know the answer to that question. We are all explorers driven to know what's over the horizon, what's beyond our own shores. And yet the more I've experienced, the more I've learned that no matter how far we travel, or how fast we get there, the most profound discoveries are not necessarily beyond that next star. They're within us, woven into the threads that bind us, all of us, to each other. A final frontier begins in this hall. Let's explore it together."
- This prompts a Slow Clap that's started by Soval, cementing the fact that Archer has earned his respect.
- Sadistic Choice: Hoshi is faced with one—destroy the verteron array and take out Utopia Colony with it, or let Paxton destroy San Francisco. She opts with the former, but fortunately, Trip is able to Take a Third Option before she carries it out.
- She Knows Too Much: Subverted when T'Pol finds out about Paxton's illness and Rigelian treatment for said illness. Rather than attempt to silence her, he practically dares her to tell his men, figuring that they're too drunk on the Kool-Aid to take her word over his. From what we see of them, he's probably right.
- Surpassed the Teacher: Harris says this of Malcolm, though most likely in jest.
- Talk to the Fist: When Trip's rage hits the boiling point, one of Paxton's mooks dares him to try something. Trip says "Okay" and slugs him.
- Terraform: Mars is in the process of it. The terraforming has already yielded a thicker atmosphere, eliminating the need for pressure suits, though they still need oxygen and thermal garments.
- Villain Respect: When Trip sucker-punches one of Paxton's mooks and sabotages part of the weapon system, Paxton is genuinely impressed. He even expected a man of Trip's principles to try something like that.
- Wasn't That Fun?: Malcolm quips this in a very sarcastic and deadpan voice after the shuttlepod almost crashes during the comet ride and even before that, they were forced to fly behind it in a very unstable manner that made him put the barf bag Phlox gave him to good use."Well, that was fun. Can we do it again?"
- Wave-Motion Gun: The verteron array on Mars is essentially a very big phaser cannon which is designed to adjust the course of comets for the purpose of terraforming Mars. The beam is wide enough to encompass Enterprise entirely, and even at 2% power it causes considerable damage. Paxton's plan is to use it to destroy Starfleet Command. Fortunately, Trip throws its aim off, and only San Francisco Bay is hit.
- Would Hit a Girl: Josiah has no problem with shooting T'Pol if Trip doesn't obey Paxton.
- You Are in Command Now: Hoshi, for the first and only time, gets to command Enterprise.
