The discovery of a derelict pod with a long-dead "human" pilot opens up a mystery. Some of the crew speculate he is the first human to invent warp drive technology, Zefram Cochrane, but DNA profiling reveal the remains are not his. Commander Tucker and Lieutenant Reed examine the mysterious pod and discover, via a floor panel, that it is spatially larger than physically possible. They also recover a device from the core which still has a weak energy signature. Shortly afterwards, a Suliban ship arrives and claims salvage rights, but Captain Archer refuses to yield it without explanation. They open fire, and beam in a boarding party, but are finally repelled.
Undaunted, Enterprise then sets course to rendezvous with Tal'Kir, a Vulcan ship. Doctor Phlox's scans reveal the dead pilot has multi-generational DNA fragments from several other alien species including Vulcan, Terrelian, and Rigelian. Seeking answers, Archer and Sub-Commander T'Pol enter Agent Daniels' cabin, and they learn that the pod is a time travel vessel from the 31st century. Meanwhile Tucker and Reed, on returning to the pod, get stuck in a recurring time-loop. This heightens T'Pol's concerns and she discusses the situation with Archer, who feels they must have more information on the Temporal Cold War.
Tholians arrive, requesting the pod and warning Enterprise of temporal radiation. Again, Archer refuses, and they leave after he threatens to destroy it. The crew, reaching the rendezvous destination, discovers that the Tholians have disabled Tal'Kir, and soon disable Enterprise as well. The Suliban arrive and a battle ensues, but they are quickly annihilated. After working through another time-loop, Archer and Reed booby-trap the pod and send it out into space, but the Tholians immediately disarm the device. Tucker then gets the temporal distress beacon to power up, and soon the future ship and its contents dematerialize. The Tholians leave, and Enterprise assists the Vulcan ship, becoming Archer's olive branch to the Vulcan High Command for their support and help.