Reuel Seven – Klaxon Dilithium Mining Facility 3 – After his forces commandeer the mining operation, Borrada refuses his son Boras the right of last kill so that he may kill the station chief in forced combat himself. Borrada and his men leave in their ships after activating a portal that folds space around Reuel Seven. The planet disappears.

San Francisco, 2388 – Starfleet Headquarters – Lt. Masaru reports to Admiral Pavel Chekhov that Reule VII is the second dilithium-supplying planet to disappear in two months. Chekhov suspects that the vanishings are related to Borrada and Syphon, a planet that did not appear on any star charts until three years earlier. Chekhov shows Tuvok a recording of Admiral Satterlee dying in a suspicious accident just moments after Satterlee relayed his belief that the Federation Council may be involved in the planet-destroying conspiracy. Unable to go through Starfleet channels to confront Borrada, Chekhov and Tuvok plan to assemble a covert team of rogues and outcasts.

As a crewmember aboard the renegade ship Icarus, shapeshifter Ragnar impersonates a Klingon captain so that the Icarus may surreptitiously beam aboard the U.S.S. Archer’s dilithium supply. When the real Klingon fleet arrives, Captain Alvarez of the Archer realizes the ruse and engages the Icarus in a firefight. However, the renegade ship successfully escapes.

Since being set up by the Federation’s Section 31, previous Icarus captain Lexxa Singh serves a prison sentence on Orion. Although deeply reluctant, Lexxa agrees to return to the Icarus and act as a clandestine agent for Tuvok after Tuvok promises to reveal new information about her presumed dead mother. Lexxa insists on bringing along her Cardassian companion Garis, with whom she rigs prison fights and splits the winnings.

Before her first day at Starfleet Academy, Cadet Chekhov visits her great-great-grandfather Pavel with her roommate Cadet Madison. Admiral Owen Paris also visits Pavel and urges him to stop his investigation into Satterlee’s death and the Syphon.

Lexxa returns to the Icarus and takes command after a phaser battle with current captain Moordenaarr ends in Moordenaarr’s death. Along with Ragnar, other Icarus crewmembers include Dr. Lucien, engineer Fixer, former Borg drone Icheb, Bajoran Jaro Ruk, Betazoid Ronara, and Prak, a mask-wearing Breen. Because of the history between their two races, Jaro takes an immediate disliking to Lexxa’s companion Garis.

Starfleet Academy – At the Admiral Nimoy Memorial, Cadet Chekhov tells her great-great-grandfather about her uncertainty over an exercise asking if she would sacrifice herself to save others.

Aboard the Icarus, Dr. Lucien has a romantic rendezvous with a tactile hologram of Dr. Lewis Zimmerman being projected from Jupiter Station. Lucien mentions her banishment from Starfleet after a scientific project resulted in her assistant’s death.

Working as an agent for Chekhov back at Starfleet Headquarters, former assassin T’Leah foils an assassination attempt on Admiral D’Agosto. Tuvok and Chekhov are surprised to discover that Starfleet security will not let them access facial recognition for D’Agosto’s would-be murderer. Chekhov hires Andorian Shree to hack the system with her telepathic powers.

Still in pursuit, Captain Alvarez and the Archer engage Lexxa and the Icarus, but the Archer is forced to stand down when the Icarus escapes into an asteroid field.

Cadet Chekhov visits Pavel in his office. T’Leah discovers that a detonation device has been unknowingly planted in the cadet’s hand through nanotechnology. Cadet Chekhov has T’Leah sever her hand and beam it out of the room. Pavel immediately beams his great-great-granddaughter to Starfleet Medical. She later receives an artificial hand.

While Ragnar, Lucien, and Fixer monitor from the bridge of the Icarus, Lexxa, Icheb, Ronara, Jaro, Prak, and Garis infiltrate tunnels below Syphon leading to Borrada’s stronghold. Following a firefight with Borrada’s men, Jaro is killed. Lexxa and the others are captured by Boras. Lexxa snaps Boras’ neck. Borrada subdues Lexxa and kills Garis when he tries intervening.

Borrada tells his captives that the portal used to fold space came to his race from the Federation over 300 years earlier. Lexxa openly wonders how that is possible since the Federation hasn’t existed for that long. Borrada explains that it took decades to discover that a second portal is required to establish a gateway. Borrada blames use of the portal for turning his people into savages, although he credits it for making them stronger. His objective is to make the Federation suffer from the portal in the same way that his people did.

When Borrada’s fleet leaves Syphon’s orbit, Dr. Lucien and Ragnar follow aboard the Icarus. Lying in wait in the asteroid field, the Archer pursues the Icarus. A damaged communications array prevents Lucien from contacting Captain Alvarez about Borrada heading to Earth. Both ships arrive in time to see space folding around Earth, cutting off the planet from the sun. Lucien and Ragnar reason that Borrada already had another portal somewhere on Earth.

Although a genetic defect prevents her from being telepathic, Ronara uses her other Betazoid mental powers to free Icheb, who takes out a guard and frees the others. Fixer resupplies the Icarus away team in Syphon’s tunnels.

Presuming that the Icarus is responsible for the space fold around Earth, Alvarez opens fire and beams a security team aboard the ship. Ragnar impersonates Chekhov to fool the away team. Believing Chekhov to be injured, Commander Petrona of the Archer beams Ragnar and Lucien into the admiral’s office at Starfleet. Tuvok nerve pinches Petrona upon her arrival. Lucien begins briefing the real Chekhov on Borrada’s plan.

Lt. Masaru reveals himself as the traitorous mole when he murders Admiral Paris in front of Chekhov. T’Leah kills Masaru before he can be questioned. Admiral Paris apologizes to Chekhov before dying. Shree uses a neural device to tap into Masaru’s brainwave activity. From Masaru’s memory fragments, Lucien is able to confirm a Federation conspiracy and learn that the second dilation portal is hidden in Masaru’s office.

Borrada and his men assault Lexxa and the others at the portal on Syphon. Lexxa seemingly kills Borrada in combat.

Lucien, Ragnar, Shree, and T’Leah rush to Masaru’s office. Alvarez and an away team beam into Starfleet Headquarters, rescue Petrona, and make their way to Masaru’s office, as well.

With the portal at Starfleet set to destroy Earth, Lucien communicates with Fixer and has him activate the portal on Syphon so that he can transport the portal from Starfleet HQ. When it becomes clear that someone has to stay behind on Syphon to operate the portal, Lexxa insists it be her since the mission is her responsibility. Fixer stuns Lexxa and volunteers to sacrifice himself instead. Icheb, Ronara, and Prak beam away with Lexxa.

As Syphon begins collapsing, Borrada rises and tries assaulting Fixer only to discover that the engineer is a hologram. Space folds around Syphon and the planet vanishes.

In the aftermath, Chekhov theorizes that someone unknown was controlling Masaru. With Lexxa mistakenly presuming that the Icarus crew’s debt is paid, Chekhov reminds everyone that they are still wanted for the theft of the Archer’s dilithium and for the attack on Alvarez’s crew. Chekhov insists that the Icarus needs to remain secret from Starfleet. Chekhov promises to help Lexxa’s crew uncover who set all of them up in return for helping he and Tuvok on future clandestine missions. T’Leah and Shree are added to Lexxa’s crew.

Back aboard the Icarus, Dr. Lucien has another virtual rendezvous with Dr. Zimmerman. It is revealed that Fixer was the assistant killed by Lucien’s work at Jupiter Station, but she recreated him as a sentient hologram. Fixer returns to the crew as Lexxa and the Icarus set off into space.