The Enterprise crew sets on a maiden voyage with a mission to return a wounded Klingon to his people.
At Rigel X, the Enterprise away team discovers an amazing multitude of alien life at a trading complex there, and their attempts to locate information on Klaang's visit are constantly interrupted by strange new sights and sounds. Archer eventually meets Sarin, who tells him of a Temporal Cold War in which the Suliban are being used to incite internal strife within the Klingon Empire. Klaang was bringing proof of this back to his High Council in order to avoid the Empire being thrown into chaos. Hidden Suliban soldiers suddenly attack, forcing Archer, Sarin and the rest of the away team to fight their way back to Enterprise. During the extremely intense firefight Sarin is killed, and later Archer is rendered unconscious from a deep blast to his leg while saving T'Pol's life.
As Archer recovers, T'Pol takes command of Enterprise despite Trip's objections, and astonishes everyone by enabling the ship to track the Suliban vessel from Rigel X, rather than ordering the ship back to Earth. After Archer resumes command they arrive at a gas giant planet, apparently losing the Suliban's trail. But T'Pol is again surprisingly helpful when she works with Archer to determine that not one but 14 Suliban vessels have recently entered the planet's atmosphere. Enterprise goes in to follow, and discovers a huge Suliban mothership, or "Helix," with 3000 lifesigns on board. They are attacked by several individual Suliban cell ships, but manage to capture one with the ship's grappler. Archer and Tucker learn to fly the stolen craft and use it to infiltrate the Helix while Enterprise hides in a dense upper layer of the atmosphere and avoids the Suliban's depth charges. Archer and Tucker find Klaang and release him while fending off the Suliban with their new phase-pistols. While Tucker takes the Klingon back to Enterprise, Archer stays behind to set off a magnetic disruptor that dismantles the Helix. Trying to stay alive while waiting for pick-up, Archer discovers a Temporal Chamber used by the Suliban to obtain their orders from a mysterious shrouded figure from the future. Archer is found by the Suliban leader, Silik, and the two struggle against each other in a time-shifted environment. Realizing he's no match for the genetically mutated Suliban, Archer tries to gain some distance by exiting the chamber, where time returns to normal. As Archer runs, Silik fires his weapon dead center into Archer, but at that moment the captain dematerializes, being unwittingly beamed back to Enterprise by a nervous Tucker using the relatively untried bio-transporter.
Leaving the Suliban behind, Enterprise warps away and successfully delivers Klaang to his homeworld. The Klingon Chancellor draws blood from Klaang, and his scientists find hidden within his DNA Suliban data proving their conspiracy to undermine the Empire. The Chancellor turns to Archer and acts hostile toward him, but Archer takes his actions as a "thank you."
Back aboard Enterprise, Archer receives orders from Starfleet that henceforth, he and his crew are to officially begin their mission of exploration. Gratefully acknowledging her assistance in the mission's success, Archer sets aside his pride and convinces T'Pol to remain on the ship as Science Officer. A course is laid in for the nearest inhabited planet, and the crew of Enterprise boldly warps toward the unknown.
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