This episode marks the real start of the Temporal Cold War.
Aboard Silik's vessel, Silik is strapped to an operating table in the temporal communications chamber. Future Guy tells Silik that the operation is going ahead because he failed in his last mission - the Klingon Empire is still intact in the 22nd century. Silik protests but Future Guy continues by saying that he won't need his enhanced vision where he is going and that he will return it when Silik succeeds. Another Suliban approaches the operating table and activates a probe that waves forwards and backwards in time as it moves towards Silik's right eye.
Hoshi and Mayweather use the turbolift to get to the Bridge for their duty shift. Mayweather complains that the previous night's film, Attack of the Killer Androids, was really bad. With 50,000 movies in the ship's database there must be something worth watching. Hoshi recommends reading a book instead. Reed greets them upon arrival and also says that he thought that the film was terrible too.
In the Captain's Mess, Archer is served by Crewman Daniels. Daniels asks why Archer ordered a course change and Archer says that they detected a stellar nursery with several ships inside, so he wants to go and say hello.
The Enterprise reaches one of the ships and Captain Fraddock responds to Archer's hail. Fraddock is escorting a group of spiritually-minded men on a pilgrimage to the Great Plume of Agosoria. Every 11 years, one of the protostars gives out a neutron blast. The pilgrims believe that it is a sacred event. The eruption is due tomorrow. Archer extends an invitation to Fraddock and the pilgrims to visit Enterprise.
The pilgrims come aboard, led by Prah Mantoos. They bring gifts of a clock that tells the time from the beginning of the Universe and a spirit, Voo-Sinteel, to be drunk during the eruption to enhance the experience. As the party moves off to enjoy a celebratory meal, one of the pilgrims lags behind, wearing a knowing smile. In the Mess Hall, Phlox compares the pilgrims' beliefs with Hinduism and its belief in the Universe going through repeated cycles of rebirth. Phlox says that he studied a number of Earth religions; he spent two weeks at a Tibetan monastery and attended Mass at St Peter's Square in Rome and was even allowed to observe the Tal-Shanar at the Vulcan consulate. When asked which religion he follows, Archer says that he tries to keep an open mind.
On the Bridge, Reed detects that the starboard targeting scanner is out of alignment, so he leaves Mayweather in charge while he fixes it. Mayweather takes the Captain's chair at Hoshi's prompting and Reed finds him studying the controls when he returns. He smiles to himself when Mayweather goes back to the helm.
In Engineering, Trip explains about the Warp 5 engine to the pilgrims in simple language. One of them turns out to be a warp field theorist. It is the alien who lagged behind earlier on. When Trip is distracted with a question, the alien moves to the other side of the warp reactor and reaches up to disconnect an antimatter junction. His arm morphs to reach the junction, revealing his identity as Suliban - it is Silik.
Fraddock hails to make sure that the Enterprise is aware of a plasma storm ahead. He suggests moving around it and T'Pol agrees. In Sickbay, Phlox demonstrates the medical scanner. The ship shakes and T'Pol tells Archer that it was caused by turbulence from the plasma storm. The turbulence grows worse. Silik smiles to himself again as Trip works on the reactor. Archer ends the tour and returns to the bridge. In the Mess Hall, Crewman Daniels looks worried. A plasma bolt causes an antimatter cascade, blowing out systems in Engineering one by one. It almost reaches the reactor when it stops short. Trip has no idea why. In the background, Silik looks satisfied.
The pilgrims return to Fraddock's ship, accompanied by Phlox. Trip summons Archer to Engineering. He has found Silik's handiwork with the antimatter junction. Trip doesn't think that any of the Enterprise's Engineering staff would have done this. Fraddock arrives onboard to speak to Archer. He spoke to all of the pilgrims and they all deny visiting the conduit. In the corridor, Crewman Daniels approaches Archer and requests to speak to him. Daniels says that he believes that one of the pilgrims is a Suliban soldier, Silik. Daniels asks to speak to Archer in his own quarters.
In his quarters, Daniels pulls out a non-Starfleet-issue case and tells Archer that he is not a Starfleet officer, before going to talk about the Temporal Cold War. To demonstrate, Daniels activates a handheld device he removes from his case. The cabin is replaced by an interactive vista of multi-coloured lines, nodes and spheres, surrounding both men. "This is how we keep an eye on what's going on", Daniels comments. He goes on to point out his time of origin, the 31st century. Daniels tells Archer that the people who command Silik are from an earlier century and can't yet materialise in the past, only transfer information.
Daniels says that the species who developed time travel technology all agreed that it could only be used for research but that the temptation was too great, hence the Temporal Cold War. He points out the trace of a group of anthropologists from 2769 observing the construction of the Great Pyramid at Giza; they follow the proper procedures as set out in the Temporal Accord. Other species choose not to follow the Accord. Daniels terminates the display and tells Archer that it was Silik who prevented the warp core breach and that he has been sent to the past to capture him. To complete his mission, Daniels needs Archer's help. Daniels asks permission to tie his Suliban tracking technology in to the Enterprise's internal sensor grid from Engineering, and for Archer's command codes. Daniels says that his group need to identify for whom Silik is working in order to stop them interfering with time. Archer says that he will need to inform some of his crew in order to assist Daniels.
In the Ready Room, Archer briefs T'Pol and Trip. T'Pol says that the Vulcan Science Directorate has found no evidence for the existence of time travel. Trip says that it would be foolish to look a gift horse in the mouth. Hoshi hails to say that Fraddock's vessel is requesting permission to dock so that some of the pilgrims can observe the Great Plume in the Mess Hall. Archer finishes the briefing by ordering T'Pol and Trip to help Daniels.
In the turbolift, T'Pol and Trip debate time travel. T'Pol says that there is a difference between keeping an open mind and believing something because you want to be true. On the Observation Deck, Archer studies the group of pilgrims, wondering which one is Silik. Phlox appears and tells Archer how he enjoyed his visit to Fraddock's ship. Archer asks if any of the pilgrims appeared out of place. Phlox says no and wonders why. Archer says that he is curious, nothing more.
In Engineering, Trip talks to Daniels. Daniels doesn't really have a brother on Jupiter Station but he is from Illinois, although not the one with which Trip is familiar. Daniels busies himself at a workstation, calibrating the internal sensors. Trip picks up Daniels' device and presses a button, causing a 3D display to activate. Daniels quickly shuts it off. T'Pol observes that one of the power relays is offline. Daniels uses a piece of technology to repair it, placing it on his fingers before walking through the bulkhead. Trip and T'Pol look at each other.
Archer arrives back at his quarters. Porthos is barking for his breakfast, which is two hours late. Archer feeds Porthos, who continues to growl and bark at nothing. Archer looks around curiously - the cabin appears empty. He then sees one of the pilgrims' cloaks on his desk. Silik's voice tells Archer not to call for help. Silik deactivates his camouflage and asks Archer who it is who is trying to find him in returning for saving the ship yesterday. Archer denies all knowledge, and Silik goes on cynically talking about Daniels' group and the Temporal Accord. Silik says that Daniels' group was responsible for the antimatter cascade - that faction is trying to alter history, not his own. The Temporal Accord is a lie. Silik doesn't know why he was ordered to save Archer, only that Daniels is a danger to the Enterprise and that Archer would best serve them by helping Silik. T'Pol signals to say that Daniels has finished and is eager to start. Silik smiles and thanks Archer before stunning him and moving off.
On the Observation Deck, Prah Mantoos says that the Great Plume is beginning and asks Phlox if he would like to recite the Prayer of Renewal with the pilgrims.
In Engineering, Daniels detects Suliban bio-signs. Silik is on C Deck, near Main Engineering. Daniels asks that Reed seal off the deck and to arrive with a security team. Silik's bio-mimetic camouflage hides him on an upper walkway; Trip sees movement out of the corner of his eye. Daniels evacuates Engineering and turns to find Silik pointing a phaser at him. Silik fires and Daniels derezzes, as if he were a hologram. T'Pol and Trip witness this, then summon Phlox to Archer's quarters when they receive no response to their hails.
Phlox revives Archer with a hypospray. Trip says that Silik killed Daniels. Archer hails Fraddock to see if any of the pilgrims has returned. Fraddock says no. Archer hails Reed and orders that all outer hatches are sealed and that security details are to be posted on every deck. Archer asks Trip to use Daniels' sensors to locate Silik while he and T'Pol visit Daniels' quarters to study the database that Archer saw earlier. The case is empty when Archer opens it. Hoshi hails to say that someone on board used the ship's comm system to transmit an encrypted message.
In Engineering, Trip can't interpret Daniels' sensor readouts. Silik opens a service hatch on B Deck, junction 59, which Trip detects. He is trying to bypass the lockout codes for Launch Bay 2. Archer meets Reed and the security team at the junction, holding Daniels' phasing device. He activates it and experiments on a bulkhead, watching his hand pass through cleanly. Archer takes Reed's phase pistol and walks through the bulkhead. On the other side, Silik is working on Daniels' device. He tells Archer not to fire in order to prevent another antimatter cascade. Archer wonders what sort of genetic enhancements Silik will receive for delivering Daniels' database to his masters. As they talk, the ship is rocked by another plasma wake. They fall to the floor and struggle, Silik losing his phase pistol. Silik tosses Archer aside before escaping in to the Jeffries tubes. On the Bridge, a Suliban shuttlepod is detected.
Silik arrives in Shuttle Bay 4, Archer close behind. Silik refuses to surrender the device, so Archer shoots it from his hand. "You may have endangered your future, Jon." Silik snarls, before camouflaging himself. Archer searches around, then hears an alarm sound. The doors to the Shuttle Bay open, blowing loose objects out in to space. Archer hangs on but loses his phase pistol. Silik removes his camouflage, steps away from the controls and with a backwards look at Archer, leaps in to the void. Archer closes the doors and repressurises the room as Silik freefalls toward the waiting Suliban shuttlepod. T'Pol hails to say that the shuttlepod went to warp but Archer tells her not to follow.
In his Ready Room, Archer studies the clock given to him by Prah Mantoos. T'Pol enters to say that the Fraddock's ship has left. Archer doesn't know how the clock works. Archer will prepare the report for Starfleet in the morning. On the Bridge, Archer asks Reed to assign new quarters to Daniels' roommate and to seal off cabin E-14. Archer looks troubled as the Enterprise resumes course. Outside cabin E-14, Reed places a large electronic lock on the door.