The Xindi weapon is in a vortex with a Xindi-Reptillian ship, upon which Dolim and two others are standing. Dolim and one of the others imagine what life would have been like if they were initially the dominant species. Dolim thinks that the Reptillians will run the show once Earth's destroyed, and they celebrate by eating mice.
On Degra's ship, the Xindi-Primate councilor tells Archer that the weapon is almost three hours away and they are closing the gap. Malcolm, noting that the shuttle is faster but less armed, asks how many ships are escorting it, but they don't know. Archer notes that the only way to destroy the weapon is from the outside, but since the schematics are coded, it's currently impossible. He decides to get Hoshi's assistance, even though she's still physically weak from the events of the previous episode.
While the Guardians decide to crank up the amount of anomalies in the Delphic Expanse to try to stop the Enterprise, Trip reports to T'Pol that he realigned the power grid to increase the deflector pulse, but it will "fry" most of the ship's systems and probably destroy it. T'Pol, despite this, insists he activate it, but Trip refuses, saying he was asked to destroy the spheres, not the ship. She points out that if Earth is destroyed, the Delphic Expanse will expand, putting other planets at risk.
On the bridge, Travis detects spatial anomalies around the sphere, indicating that its cloaking barrier (which usually prevents it from showing up on the sensors) is faulty. In sickbay, Phlox tells T'Pol that the space around the sphere is changing. She wants to get within a kilometer of the surface of Sphere 41, but he tells her that the radiation would kill them all unless they manage to destroy the Sphere within minutes.
On Degra's ship, Archer asks Hoshi how she's doing with the decryption, but she's still sickly and wants to see Phlox. When Archer tells her Phlox is unavailable, she becomes sad and claims to be at fault for giving the Reptillians the codes. Archer tells her she had that choice, but she thinks she ought to have fought harder. He simply tells her to get back to her job, which she does. Meanwhile, Dolim and the others prepare to launch the weapon.
Trip then shares a new plan with Travis: he knows how to destroy the sphere without destroying the Enterprise, but it requires taking power from the impulse engines. Malcolm tells Archer that he will not be able to transport directly onto the weapon's control panels because of the deflector shielding. Archer and Hoshi (who Archer brings because she's been on the Xindi weapon before) leave, with Archer telling Malcolm that he doesn't plan to die. He finds himself on a balcony, where Daniels shows a picture of himself seven years or so later, revealing that Archer will make history then.
Enterprise arrives at Sphere 41 and the anomaly is growing. Phlox gives everyone a compound to keep them healthy and tells them to stay in the disturbance for fifteen minutes tops. Back on Degra's ship, Archer tells Hoshi that they need to disable the reactor at a specific point inversion sequence, but he doesn't know the sequence, and if they get it wrong, the safeguards will kick in, rendering it impossible to destroy. Hoshi has the sequence, but hasn't decrypted it. A Xindi tells Archer that they're near enough to isolate the weapon's signature, and the weapon is being escorted only by Dolim's ship.
On his ship, Dolim is informed that Degra's ship is less than twenty minutes behind him. Dolim tells his crew to start the firing sequence once they exit the vortex. The Xindi then notice that there are no Earth ships around, but only one unarmed orbital station. Enterprise has entered the disturbance and are prepared to fire up the thrusters, but Trip is starting to develop a rash due to the anomaly.
Dolim's ship exits the portal and heads for Earth, while Archer tells Malcolm's team to prepare to the weapon. The Xindi notices that Dolim's ship has changed course for a space station, which Archer recognises as a research station called Yosemite Three. They try to hail them, but can't because of the weapon's destruction wave. When Enterprise reaches the sphere, T'Pol instructs them to drop to two thousand meters. Trip tells Phlox about his rash, with Travis noting that he also has it, but Phlox tells them that it's a normal side effect and they'll be fine if they don't scratch it.
Dolim quotes the Guardians' orders to destroy all human colonies when Earth is destroyed and he and his crew blow up Yosemite Three. Trip fires at the sphere on T'Pol's command, while the engineers check the systems. Three Sphere-Builders appear out of nowhere and attack with balls of ions. Then, they start shutting down the power systems in hopes of shutting down the deflector pulse. The effects are noticed on the bridge, and Phlox counts nine of them.
Dolim prepares to intercept Degra's ship, while the Arboreal tells Archer that the intercepting ship is firing up its weapons, and there's another ship asking for Archer. It turns out to be Shran, who offers assistance. Meanwhile, the deflector pulse is diminishing and the MACO weapons pass through the Sphere-Builders. Corporal Kelly orders everyone to reset their weapons to a modulating frequency, which they do, forcing the Sphere-Builders to retreat, but they continue disrupting power systems at another console.
The Kumari escorts Degra's ship, while fighting off the Xindi ships. Archer and his boarding party beam to the weapon and kill the Reptillians, then Archer begins the overloading process. Dolim discovers that the boarding party are onboard the weapon, then more Reptillians appear and start fighting the boarding party. Phlox tells the others that their time has ended and T'Pol orders an evacuation. Then, the spheres start collapsing and the Sphere-Builders on Enterprise disappear. Eventually, all the spheres are destroyed.
Shran discovers that Dolim has beamed to the weapon and orders all weapons targeted on Dolim's ship's starboard engines, thus destroying it. Archer asks Malcolm for the charges, and Malcolm is unsure, but Archer insists. He puts the charges on the reactor and detonates them, then climbs down the shaft to flip the final switch, but runs into Dolim. They fight, then Archer puts another charge on Dolim's back, killing him. Then, the weapon blows up.
Back on Enterprise, T'Pol notes that the long-range sensors are detecting no spheres or anomalies, and the cloud-like formations they detected earlier are going away. The crew then tries to communicate with Archer, while T'Pol reveals her age (65) to Trip, noting that some Vulcans consider this detail "intimate". The two ships meet and Malcolm explains that Archer didn't make it out in time. Enterprise docks with the Xindi-Acquatic cruiser, where the Primate tells T'Pol that they will be returned to Earth within a day. He also notes that the Xindi-Reptillians will have to accept that they were being exploited.
T'Pol and Phlox talk in sickbay, but there's a dreary mood, since the crew thinks Archer is dead, Phlox's pets dislike the new environment, and Porthos is unhappy too. The Enterprise heads back to Earth, leaving the Xindi vessel behind, and Hoshi is almost totally better and returns to work. They arrive at Earth and admire it, but Hoshi is unable to reach Starfleet Command. Scans show that the orbital platforms are gone, and and the Lunar One Colony also isn't responding. T'Pol sends Trip and Travis in a shuttlepod to San Francisco and at first things seem okay, but then it turns out they've apparently gone back in time to WWII. Archer is then seen being treated at a Nazi hospital, by an alien in Nazi clothes.
Tropes in this episode include:
- Admiring the Abomination: From the villain's POV. Dolim briefly admires Earth's beauty, noting that the Aquatics would love the oceans.
- The Apple Falls Far: While Hoshi and Archer are on a catwalk inside the Xindi superweapon, a PADD goes flying over the edge. Shocking not because of the depth revealed (three people have fallen in already) but because it had their instructions on how to destroy the superweapon.
- Big Damn Heroes:
- Naturally, Shran shows up to be Archer's backup.
- Notably averted by Starfleet and the Vulcans. That fairly large armada we see welcome Enterprise back in two episodes sure would have been useful against the Xindi weapon and the one ship escorting it.
- Bittersweet Ending: The Earth is saved, the Xindi are dealt with, and Archer survived the explosion... but there are Nazi aliens, and the crew thinks Archer is dead.
- Call-Forward: For possibly the first time in-universe, the navigational deflector dish is used as a Wave-Motion Gun, which we'll see again in TNG, DS9, the movies, and onwards.
- Cliffhanger: After fourteen years of season-ending cliffhangers, ENT has perhaps the most bizarre one to date for the franchise. The NX-01 returns to Earth, and is met with nothing but radio silence. Trip and Travis take a shuttle to San Francisco, only to be fired on by P-51 Mustangs. Elsewhere, Archer is badly wounded, but alive in a German field hospital, where he is observed by a group of Nazi officers...one of whom is an alien...note
- Combat Pragmatist: Archer defeats Dolim, who's twice his size, by strapping a bomb to his back and pushing the remote button. Dolim has a brief "Oh, Crap!" moment before he's all over the walls.
- Continuity Nod: Back in "Doctor's Orders," Phlox was the only one who could remain awake in the anomaly. Now he's the only one whose skin doesn't degrade during the attack on Sphere 41.
- Danger Deadpan: Trip works amazingly under pressure.Phlox: In about five minutes, everyone on board is going to start dying!
Trip: No pressure. - Disney Villain Death: Several Reptilians on the weapon suffer this.
- Even Evil Has Loved Ones: As Dolim goes on about how much better things would've been had Reptilians been the dominant Xindi species, one of his mooks remarks their "Avian brothers would still fill the skies."
- Exact Time to Failure: And Trip works his magic Just in Time.
- Failed a Spot Check: Even from high altitude, Travis thinks that 1944 San Francisco looks "pretty normal." This
◊ is what they see. The fact that none of San Francisco's current or future skyline exists doesn't tip them off. - Final Battle: For the Xindi Arc. It actually takes place on two fronts, with Archer, Malcolm, and Hoshi boarding the Xindi weapon and T'Pol leading Enterprise to disable a control sphere.
- Fire-Forged Friends: Of a sort—while mourning the (supposed) death of Archer, T'Pol takes a moment to console Porthos, whose existence she's disapproved of since Enterprise launched.
- Fragile Speedster: Degra's ship is fast enough to catch up to the Reptilians and the Weapon, but it's no match for them on offense or defense.
- Gainax Ending: One of the most random, left-field endings in all of Star Trek.
- Gallows Humor: Before undertaking the mission to destroy the sphere, which could prove fatal, Phlox cheerfully bequeaths his belongings to his extended family, stating it's another one of the things that brings Denobulans joy.
- Get A Hold Of Yourself Man: No hitting involved, but Archer does have to shake Hoshi a bit to bring her back to her (addled) senses.
- Gory Discretion Shot: Though unusually gory for Star Trek; Dolim's blood gets splattered all over a column next to Archer.
- He Didn't Make It: Malcolm telling Trip about Archer's (supposed) death.
- Heel–Face Turn: The Insectoids quickly rejoin the Council after realizing that Dolim betrayed their councilor. Mallora is also confident that the Reptilians will eventually rejoin as well once they understand that the "Guardians" had nothing but empty promises.
- Heroic Sacrifice: Everyone on Enterprise thinks that Archer pulled one. Technically, he did, but was unknowingly pulled out at the last second.
- Horror Doesn't Settle for Simple Tuesday: T'Pol's log entry gives the date in which Earth was nearly destroyed as February 14 (Valentine's Day).
- It's All My Fault: Hoshi blames herself for giving the Reptilians the third code, even though she was drugged.
- Keystone Army: The destruction of Sphere 41 triggers a pulse which destroys the next sphere, and this continues until the entire network is annihilated.
- Kick the Dog: Dolim takes a moment to destroy an unarmed research station in Earth orbit. No reason. He just wanted to get a head start on killing all humans.
- Last Stand: The Sphere-Builders come aboard Enterprise and try to sabotage the ship in order to preserve their future.
- The Needs of the Many: Trip tells T'Pol that his modifications are likely to destroy Enterprise in the process of destroying the control sphere. She reminds him that, should they fail in their mission, and Archer fails to destroy the weapon, the Expanse will continue to grow and encompass hundreds of worlds, including her own."Your world is no longer the only one in jeopardy."
- New Era Speech: Dolim gives one to his minions, right before they chow down on some mice."Once Earth is destroyed, the Reptilians will take their rightful place at the head of a new Xindi Empire."
- Not So Stoic: Despite being a Vulcan, who usually never express emotion, T'Pol speaks affectionately to Porthos and pets him.
- Outrun the Fireball: Archer races to get away from the core of the weapon seconds before it explodes.
- Pre-Mortem One-Liner: As Phlox's countdown expires, he says "That's it, time's up!" To which Trip replies "It sure is!" Cue Trip initiating the final pulse that destroys the sphere.
- Red Shirt: The Sphere-Builders take out some guy in Engineering and several MACOs in the corridors, though it's not said if they're killed or just KO'd. On the other hand, a MACO is most definitely killed on the weapon.
- The Reveal: After three seasons of Trip trying to get T'Pol to reveal her age, she finally says she's 65, after Trip makes an offhanded remark that her cracked skin makes her look like an old oil painting.
- Scotty Time: Not just for Trip—everyone's on a deadline this time.
- Sticky Bomb: Archer uses them to disable the weapon, as well as a spare one to finish off Dolim.
- This Cannot Be!: The Sphere-Builder woman is perplexed as to why the favorable timelines continue to fade, even as the weapon closes in on Earth.
- Uncertain Doom: It's not clear if the Sphere-Builders who start choking and vanish when the anomaly network is destroyed have retreated back to their realm or disintegrated because they can't survive our universe's environment.
- Video Will: Phlox records one to be sent to Doctor Lucas, should he not survive.
- Villainous Breakdown: Dolim goes through this as Archer activates the weapon's Self-Destruct Mechanism.Dolim: What have you done?!
- Writers Cannot Do Math: A Reptilian reports that there are seven humans aboard Degra's ship, even though there are only six (Archer, Malcolm, Hoshi, and the three MACOs. Unless Daniels is aboard...).
- You Have GOT to Be Kidding Me!: Travis's reaction when Trip tells him that, to keep the ship from blowing up, he'll need to shut down the impulse engines, meaning Travis must get them to the sphere on thrusters only.
- You Have to Believe Me!: Once again, Daniels tells Archer that he's too important to history to sacrifice himself — and, once again, Archer tells him to bugger off.
- You Owe Me: After drawing the Reptilians away and allowing Archer to begin his assault, Shran says as much:"And tell Archer we're not even anymore. He owes ME!"
