Season 3 - Episode Guide

Enterprise penetrates the Delphic Expanse hunting the Xindi who attacked Earth, threatening to exterminate humanity. Captain Archer and Trip attempt to learn about the mysterious and antagonistic race. But their zeal to capture a Xindi leads them into a trap.

Waves of spatial anomalies pervading the Delphic Expanse distort the laws of physics. They cripple the Enterprise disrupting power, weapons, and computer systems while searching for the Xindi. These destructive distortions leave the ship's stores vulnerable to Ventaxian pirates who loot critical supplies.

Enterprise's ongoing pursuit of the Xindi leads to an investigation of an abandoned Xindi vessel on a jungle world. A highly contagious mutagenic virus infects Archer, Hoshi, and Reed and rapidly mutates them into the planet's primal and extinct native beings, the Loque'eque, but T'Pol is unaffected. As Phlox searches for a cure, Trip and T'Pol negotiate with aliens determined to kill all those infected.

Archer, Trip, and Reed return from an alien barter town with Rajiin, an alluring woman seeking to escape her life as a sex slave. But once on board, her beguiling sensuality proves irresistible to the Enterprise crew. She uses her alien mental powers on them to steal biometric data about humans so her Xindi overlords can make a bio-weapon. Two Xindi ships attack the NX-01 to retrieve Rajiin. Meanwhile, Trip and T'Pol attempt to synthesize trellium-D to insulate Enterprise from further destruction by the spatial anomalies of the Delphic Expanse. 

When Enterprise responds to a distress call from the Vulcan cruiser Seleya, stranded in the Delphic Expanse, Archer and his boarding team (T'Pol, Reed, and Hawkins) arrive on board to find its crew in a deranged, raging, zombie-like state that quickly manifests in T'Pol as well. 

A powerful and lonely telepath named Tarquin begs Hoshi to visit his faraway planet. Smitten with her, he offers to part with crucial intelligence on the Xindi only after she visits. But when Enterprise returns to pick up Hoshi, Tarquin refuses to let her go. He wants her to be his new Companion.

Archer, Reed, and MACO Major Hayes infiltrate a Xindi-Sloth industrial colony that synthesizes the vital explosive material for the Xindi super-weapon that will attack Earth. The trio kidnaps the plant foreman, who allies with them once he learns of the Xindi council's attack on Earth. Elsewhere, Trip, T'Pol, and Dr. Phlox test captured Xindi firearms to create better defenses against them.
 

After an accident on the Enterprise in 2153, a spatial distortion leaves Archer with a puzzling form of amnesia due to interspatial parasites and unable to form new long-term memories. He wakes up every day not remembering anything from the day before. At one point, he is further confused about finding himself in the future aboard an Enterprise commanded by T'Pol. Twelve years into the future, he wakes up one morning and is stunned to learn the outcome of the human-Xindi conflict. After destroying Earth, the Xindi continued searching the galaxy, determined to annihilate all Humans. The remnants of humanity have settled on the distant planet Ceti Alpha V. Now, Archer learns that he may be the key to undoing this entire tragedy if Phlox's new treatment destroys the parasites without harming him.

The crew investigates a world within the Delphic Expanse with a civilization closely resembling America's 19th-century Wild West. A previously unknown colony of humans is oppressing an alien race called the Skagarans. Archer becomes embroiled in a cultural conflict and sets out to learn how both races got there.
 

Trip suffers a catastrophic injury in an accident that disables Enterprise inside a hazardous space cloud. His only hope for survival is a transplant from a clone or "mimetic symbiont" which Phlox grows from one of his exotic creatures. Phlox and the crew named the clone Sim. But his rapid growth and replication of Trip's behavior alarm the crew. Archer faces an ethical dilemma as the clone gains sentience and does not want to die from harvesting his organs for Trip's survival.

Acting on a tip from Daniels, Archer and T'Pol time-travel to the year 2004, where the Xindi are building a secret weapon in an abandoned Detroit factory. They must stop the Xindi from destroying Earth with a biological weapon.

After Archer rescues them from their crippled vessel, the Triannons take the Enterprise crew hostage. These alien religious zealots plot to use the ship to eradicate heretics on their homeworld.

Andorian Imperial Guard Commander Shran arrives in the Delphic Expanse and proposes an alliance with Archer, offering to help steal the Xindi's superweapon. Elsewhere, Lt. Talas, an Andorian officer with her own agenda, helps Lt. Reed repair the Enterprise's damaged weapons systems.

Archer seeks to destroy the superweapon the Xindi are constructing by creating an elaborate ruse to fool its designer, Degra, into revealing its hiding place. Archer and Degra are in a shuttle. With Degra suffering from memory loss, Archer tells him they escaped together from a prison and that the Insectoids took power after destroying Earth.

Lt. Reed and MACO leader Maj. Hayes feud over training drills which disrupts Archer and Phlox's investigation of a rescued alien near a spatial anomaly. The dying alien refuses to disclose his motives for exploring the anomaly. As Archer tries to unravel the mystery surrounding the alien, long-simmering feelings explode between Reed and Hayes. Trip's interest in a pretty MACO corporal sparks a heated exchange with T'Pol, who eventually confesses her feelings for Trip.

Archer places Dr. Phlox in control of the Enterprise when the crew requires sedation to survive a trans-dimensional disturbance. This mind-altering section of the Expanse is lethal to humanoids. But Phlox's Denobulan physiology doesn't entirely shield him from its effects, causing hallucinations. 

The discovery of unhatched Xindi-Insectoid eggs inside a crashed vessel brings out the paternal side of Archer, who alarms the crew with his obsessive determination to save the embryos.

After pinpointing the site of the Xindi doomsday weapon, Archer plans to sacrifice himself to destroy it. Daniels arrives and takes him 400 years into the future to show him the far-reaching consequences of the Enterprise crew's actions and to beg Archer to reconsider.

While dissension among Xindi ranks festers, Degra gets Archer returned to Enterprise. Archer considers compromising his morals to restore Enterprise's warp capacity after a fleet of Xindi-controlled warships cripple the vessel's engines. Sacrificing his ethics, he attacks an innocent alien ship to get their warp coil to repair the Enterprise's engines and intercept the Xindi superweapon. Meanwhile, T'Pol grows increasingly volatile, prompting her to confide a troubling secret to Phlox. Trellium-D exposure led to her addiction, with withdrawal symptoms weakening her emotional control.

Archer persuades Xindi weapon-designer, Degra, to examine evidence of the plot to pit the Xindi against Earth to prove humanity is not his enemy. When Archer demonstrates they've been manipulated, Degra offers to attempt to delay the launch of their superweapon. Meanwhile, the crew mourns their lost mates, with Trip still coming to terms with his sister's death and wrestling with the recent death of a subordinate. T'Pol confronts her substance addiction to trellium-D.

Before attempting to use a Xindi subspace corridor to reach the Xindi council, the Enterprise crew faces a bizarre encounter with their own descendants on an Enterprise. Captained by T'Pol's son Lorian, the ship warns Archer of an alien attack by Kovaalan ships. Enterprise escapes into the subspace corridor, but attack damage destabilizes the corridor, causing a time shift with the ship emerging in 2037. Will foreknowledge change anything?

Enterprise arrives at the location of the Xindi Council, and with Degra's help and Hoshi translating, Archer makes his plea before the five Xindi races. Archer must prove that the Sphere Builders have been lying and Humanity is not their enemy. While the Primates and Arboreals are already aware of the truth, convincing the other three races will not be easy. The Reptilians and Insectoids refuse to even listen to Archer. Meanwhile, seeing a diminished number of successful timelines with Earth destroyed, the Sphere-Builders arrange a secret meeting with the Reptilians. They seize the Xindi weapon and launch it, protected by five Insectoid ships. Elsewhere, T'Pol and Reed lead a mission inside a Sphere to retrieve its memory core for information about the Sphere network inhabiting the Expanse.

The Reptilians kidnapped Hoshi to brainwash her into cracking the weapon's arming codes. Meanwhile, Archer and his new Xindi allies (Arboreals, Primates, and Aquatics) attempt to stop the arming of the superweapon aimed toward Earth, launching a full-scale assault on the device. When the Sphere-Builders see the weapon is about to be destroyed, they cause at least one sphere to emit massive spatial anomalies destroying many ships. Reptilians and Insectoids escape with the weapon through a subspace vortex heading for Earth. 

Archer tries to coax a traumatized Hoshi into using her decryption skills to disable the Xindi doomsday weapon before the Reptilians can use it to destroy Earth. Archer risks his life in a dangerous gambit to intercept the superweapon, sneak by the Xindi Reptilians aboard, and disarm it from inside. Meanwhile, the Enterprise embarks on its own desperate mission to cripple the rest of the spheres.