When the Enterprise crew discovers a mysterious, futuristic vessel adrift in space, Captain Archer orders it brought onboard for further investigation. Inside the craft, the crew is shocked to find what is apparently a human body, charred beyond recognition. Trip and Reed take a closer look at the interior of the ship, and discover that it is much more spacious that it appears. They also discover a "black box" device within the depths of the ship and prepare to bring it up to Engineering for more research.
Before they can explore much further, however, Enterprise is hailed by a Suliban ship. The Suliban claim that the futuristic ship belongs to them and demand that Archer turn it over immediately. When he refuses, the Suliban open fire and beam a pair of soldiers onboard Enterprise. The soldiers attack Trip and Reed and attempt to break into the launch bay containing the vessel. Enterprise manages to disable the Suliban ship's weapons, but before they can do any more damage, the soldiers beam back to the ship and the ship cloaks, disappearing from view. Archer, however, can't help but wonder why the Suliban want the mysterious vessel so badly.
Post-battle, Trip and Reed examine the black box device, hoping that it can tell them something about the strange vessel. Meanwhile, Dr. Phlox has some curious news — his autopsy of the charred corpse reveals genetic material belonging to several other species, including Vulcans. He surmises that the individual seems to be the result of several generations of interspecies breeding. Archer and T'Pol decide to pay a visit to Daniels' old quarters, hoping that his futuristic database might give them some answers.
Indeed, the database contains what appears to be a schematic for the ship. Theorizing that the ship and its occupant are from the future, Archer has a troubling revelation: if the Suliban take the ship, they could dismantle it and learn how the engine works. This could change the course of the Temporal Cold War. Before he has time to ponder this further, Enterprise is approached by another vessel. This one belongs to the Tholians, a xenophobic, non-humanoid species. The Tholians say they have been sent to retrieve the futuristic vessel, and claim that its temporal radiation could be dangerous to the Enterprise crew. When Archer refuses to turn it over, the Tholians lock on to Enterprise with a tractor beam. Archer, however, threatens to destroy the futuristic vessel and the Tholians retreat.
Trip and Reed work to unlock the mystery of the black box device, but as they do, they suddenly find themselves locked in a time loop, repeating their actions over and over. Archer wonders if this is the "temporal radiation" the Tholians referred to and orders the launch bay sealed off until further notice. He decides that the best course of actions is to rendezvous with the Vulcans and have them take the futuristic vessel back to Earth.
As the Suliban vessels approach Enterprise yet again, Trip finally determines that the black box device is actually a micro-transmitter — some sort of emergency beacon. As Enterprise approaches the Vulcan rendezvous point, the Suliban ships attack. And when the Vulcan ship comes into view, it's apparent that it has been attacked as well — the crew is alive, but the vessel is completely disabled. Suddenly, a group of Tholian ships emerge from the wreckage, firing on Enterprise. The Tholians catch the eye of the Suliban, who begin firing on them. Entrprise is now caught in a crossfire, so Archer orders Trip to activate the emergency beacon, hoping that whoever built it might send help. Meanwhile, he and Reed will arm one of Enterprise's torpedo warheads manually.
As they work to arm the torpedo, the battle between the Suliban and the Tholians rages on. Suddenly, Archer and Reed find themselves caught in another time loop. They work against the clock and finally manage to arm the warhead ... which the Tholians, who have beaten the Suliban, quickly neutralize. Luckily, Trip has managed to activate the beacon. As the device powers up, it suddenly vanishes, as does the futuristic vessel and the humanoid corpse. Everything has dematerialized ... but it's not aboard the Tholian ships. Realizing that their quarry has vanishes, the Tholians retreat.
In the aftermath, Archer and his crew are left to wonder about the origins of the future ship and its contents. For now, it will all remain a mystery.