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Enterprise navigates into a stellar nursery hoping to make contact with some of the alien vessels detected among the colorful gases and protostars. Finding a transport vessel escorting a group of alien pilgrims to the "Great Plume of Agosoria," a protostar which emits an epic burst of energy every 11 years, Captain Archer decides to caravan with the pilgrimage ship, and invites the group for a social dinner onboard Enterprise. Relations fare well among the starship crew and the pilgrims culminating with Commander Trip Tucker giving a guided tour of the Enterprise engineering bay. As the group listens attentively to Trip's oversimplified explanation of the warp engines, one pilgrim silently slips behind a bulkhead unnoticed. He opens a panel and dislocates his limb in order to disconnect a conduit within — he is a Suliban. After the disguised invader rejoins the group, the entire ship is suddenly rocked by a powerful plasma storm within the stellar nursery. Unsuccessfully attempting to steer clear of the storm, Enterprise is repeatedly hit with plasma lighting, severely damaging the warp manifold and starting a disastrous antimatter cascade traveling towards the reactor. Instead of completely destroying the ship, though, the cascade is suddenly stopped dead at the very console the Suliban tampered with moments before.

After the jostled pilgrims return to their ship, Trip informs Archer of the recently discovered separated conduit, and that although it's what saved the ship, no one is taking responsibility for its disconnection. Perplexed, a sullen Archer is approached by Crewman Daniels, a steward in the Mess Hall, who reveals he is not really a member of Starfleet, but a soldier from 900 years in the future. Taking Archer to his quarters, Daniels uses a futuristic device to project a holographic "temporal observatory." Daniels claims he was sent to track and stop Silik — the same Suliban whom Archer fought on the Helix during the ship's first mission — from altering history, but he requires a portion of the Enterprise's power and equipment to operate his futuristic tracking technology. Archer discusses Daniel's proposal with a stunned Trip and the ever-skeptical T'Pol, ultimately deciding that in case a "Temporal Cold War" actually does exist, it would be best to give Daniels the aid he needs.

Trip and T'Pol help Daniels set up his tracking devices in Engineering and are amazed at his futuristic technology, particularly a device that allows its operator to literally walk through walls. Meanwhile a suspicious Archer attempts to seek out Silik from the group of pilgrims, who have returned to the Enterprise Mess Hall in order to gain a better view of the rapidly approaching Plume of Agosoria. But when Archer returns to his quarters he is ambushed by the awaiting Silik. Insisting someone else is actually the one trying to alter history, Silik claims to be there to stop whomever it might be and needs Archer's help in identifying the unknown soldier. In an attempt to gain Archer's trust Silik confesses to having disconnected the conduit and saving Enterprise, but while Archer denies knowing who Silik is referring to, T'Pol announces over the com that Daniels' modifications in Engineering are complete, which unwittingly provides Silik with the information he required. No longer needing him, Silik stuns Archer into unconsciousness.

While waiting for Archer to arrive, Daniels' tracking device alerts him to Silik's presence within Engineering, and he insists Trip and T'Pol immediately leave to bring reinforcements to help contain Silik. As the two comply and leave Engineering, they witness Silik murder Daniels without hesitation, then use his genetically enhanced camouflaging ability to disappear from sight. Awakened by Dr. Phlox, a sore Archer orders every outer door and hatch sealed, and security posted on all decks to prevent Silik's escape. Then confirming his suspicion, Archer takes T'Pol into Daniels' quarters and discovers that the device Daniels used to project the Temporal Observatory has been stolen, deducing it was probably Silik's mission in the first place. Silik is detected by Ensign Hoshi Sato as he attempts to bypass the lockout codes for Launch Bay One, while Trip helps Archer by giving him the phasing device he witnessed Daniels use earlier. Archer uses it to walk through a bulkhead wall, catching Silik by surprise, when suddenly both men are violently rocked as Enterprise experiences heavy plasma turbulence from the much anticipated Plume of Agosoria. Silik seizes the moment to escape inside the Launch Bay, quickly followed by Archer, who, rather than letting Silik have it, opts to shoot Daniels' device out of Silik's clutched grasp. Seeing the device is destroyed, Silik camouflages himself and flees, gaining enough time to open the Launch Bay doors. Holding on to a handrail as the ensuing vacuum decompresses the bay of air, Archer watches as Silik steps to the edge of the opening and jumps out of the ship headlong into the cloudy depths of the stellar nursery. Saving himself from being sucked into space after Silik, Archer climbs into a control room and repressurizes it so he can breathe again. T'Pol comes over the com, requesting to follow Silik who has just been picked up from space by a Suliban cell ship. Archer denies T'Pol's request, opting to let the conniving Silik go as he failed to get what he came for anyway. Before retiring to bed, the exhausted Archer orders Daniels' quarters to be sealed off indefinitely, as a safeguard against any other unknown powerful and mysterious devices that may lie within.