Dylan, Harper, and Rhade are on the Maru hunting down cobalt and nickel smugglers, while Beka and Trance are on the Andromeda following other leads. Harper and Rhade are sparring verbally, to Dylan's annoyance. A courier ship finds them, and asks for confirmation that Harper is aboard. When they give this confirmation, three Templar ships open fire on them, damaging the Maru's missile tubes. Dylan tells Harper to prepare the escape pod.

The Maru's escape pod launches, and it is quickly destroyed by the Templars.

The Templars board the Maru, and search the ship, but Harper, Rhade, and Dylan are hidden behind a holographic wall and escape detection. The Templars' conversation reveals that they want Harper alive. One of them takes the helm of the Maru, and pilots it with the rest of the Templar ships to a planet.

Harper realizes he has left the control for the holographic wall on a counter outside the hiding spot. He tries to retrieve it, but he is caught by the Templars. Rhade tells Dylan to stay hidden and tries to rescue Harper, but is also captured. The Templar Lieutenant uses the control to drop the holo-wall, but Dylan manages to stay hidden.

The Andromeda is at a scheduled rendez-vous, but the Maru is not there. Since they are hot on the trail of a smuggler, they drop a beacon and continue.

Harper uses his sub-vocal transmitter to contact Dylan as they are being taken into the Templar's compound. They are taken to the Patriarch, who orders Rhade's High Guard uniform torn off him, as he considers a Nietzschean a disgrace to the uniform. He also has sleep deprivation devices attached to Harper and Rhade's foreheads. He informs them that he is having a bridge built to the planet's moon, which is why he needs Harper, one of the brightest engineers in the Commonwealth. He orders the Templars to begin torturing Rhade.

Dylan, trying to find a way into the compound, shoots a steam pipe to cause a distraction, and sneaks by the guards.

Harper offers to help the Patriarch, in order to save Rhade. He points out that he noticed that the bridge and the moon will not be aligned for over 200 years, therefore the Patriarch must be building a bridge across time, which is why Harper's genius is required. The Patriarch agrees to spare Rhade's life, but orders him thrown in the "scrubber".

A guard finds Dylan, but Dylan gets the jump on him and knocks him out.

Rhade is in the scrubber, a small, unpleasant chamber with a large fan in one wall. The Templar Lieutenant lets him out to work, and Rhade thanks Harper for saving his life. Harper introduces him to an old mentor of his, Woody, who has also been captured by the Patriarch.

Andromeda is chasing a smuggler's ship, but encounters a minor glitch with her thrusters, causing a brief stall. Andromeda notes that Harper was supposed to fix this, but she is able to keep on the smuggler's tail.

Dylan, wearing a guard's uniform, finds Harper and Rhade, and compares notes with them. He informs them that he has stashed some weapons outside, but wants to know what the Patriarch's plans are before making his move. Harper says that he is confident that he can find out, given some time, and Rhade says that he can "tough it out". Dylan agrees to the plan, but warns Harper not to let them finish the time bridge. He wants access to the Patriarch's files, and Harper says that he can arrange this.

Harper tells the Patriarch that he knows what his problem is: They need to use a tachyon to create the time dilation, but they do not know how to make a tachyon. Harper claims that he knows how to do so, and, in the course of the conversation, palms a data card from the Patriarch's desk.

The Patriarch knows of Harper's previous time-travel experiments involving the calimelon, but points out that this is his opportunity to take it farther, and be known for doing something on a larger scale. Harper questions the Patriarch's motives, but the Patriarch appeals to Harper's pride. Harper says that if this was the next step in scientific evolution, others would be discovering it, too, but then he realizes that between his experiments and the Patriarch's, this may be the case, meaning that the Magog and others may even be closer. He resolves that he must be the first to succeed.

Harper drops the data card at Dylan's feet as the prisoners are being moved. Dylan reviews it, and finds that the Patriarch is using a lot of cobalt and nickel in the construction of the bridge, leading to the conclusion that he is behind the smuggling. He reviews the Patriarch's plans, and discovers that the bridge and the moon will only be aligned for a single day, which makes him wonder aloud about the purpose of the project. The Patriarch interrupts him, claiming that the moon holds "salvation", as the Commonwealth is not prepared for the war with the Magog. Dylan finds himself surrounded, and surrenders to the Patriarch, who puts him to work, telling him that Harper has already done what was needed.

Rhade tells Dylan to make his own escape, but Dylan is unwilling to leave the others behind. He hears about the scrubber, and learns that it draws in air from the outside.

Andromeda is chasing a smuggler ship, and Beka anticipates some of the tricks the pilot will use to try to shake them. She is following close, and an attempt to reverse thrusters encounters the same glitch as earlier, and Andromeda rams the smaller ship, destroying it. In the wreckage, Andromeda finds thousands of small arms among the cobalt and nickel. Beka decides to return and check the beacon.

Dylan organizes a sit-down strike to get the sleep deprivation devices removed. The Patriarch orders Dylan killed, but Harper protests, and indicates that the devices hinder productivity, and he could even complete the time bridge earlier if they were removed. The Patriarch agrees to remove the devices, but has Dylan thrown in the scrubber.

Woody brings Dylan his water rations in the scrubber, and distracts the guard long enough for Dylan to take a tool from Woody's belt, cut through the grating, and escape the scrubber to the outside, through the ducts. He recovers the stashed weapons and gets to the Maru and away. He scans the moon on the way out of the system, and finds housing and training facilities, although they are sparsely populated. He comes under fire from Templar ships, and manages to get away, but passes out as he reaches Andromeda's beacon.

The Andromeda picks up the Maru and Dylan is taken to Med Deck. He compares notes with Beka, and they realize that the Patriarch is building an army which he can bring back from the future.

Harper has almost completed the time bridge when Andromeda arrives in the Templar system, staying out of sensor range. Dylan assumes that the Patriarch plans to use his army to pick up the pieces after the Magog invasion. He tells Andromeda to prepare to destroy the bridge, but he wants to get Harper and Rhade out first.

Harper is pleased with his success, and ready to activate the bridge, but Dylan radios him and tells him to destroy it. Harper protests that he needs to know if it really works, "in the name of science". Dylan and Rommie approach on foot, taking out the Templar guards as they go. Harper activates the time bridge, and it works. A gate opens, and a Magog drops through, only it is more "evolved" than Magog that have been seen previously. Several more follow, carrying guns, and attack. Harper realizes that the bridge has to be closed, but the Magog prevent him. One of the Magog recognizes Harper as having worked with Red Plague (Rev Bem), who was his great-great grandfather, and the first to "control his hunger". He sprays a substance on Harper, and tells him that he looks forward to their children. Harper realizes that the Magog are marking people that they plan to infest. The Magog kill several people, including Woody and the Patriarch.

With Magog still coming through the gate, Rhade takes a gun from one of them and joins the fight. Dylan and Rommie move to rescue Harper, although Dylan is furious with him, and demands that he find some way to destroy the bridge. They send Rommie through the Magog to open an access panel, and Harper and Dylan use one of the components to fire a beam into it, closing the gate, and they make their exit.

Back on the Andromeda, Trance tries to reassure Harper that the situation was not all his fault, and things are not necessarily as they seem. The Magog did not necessarily come from their own future, demonstrating that the Magog win, they may have come from an alternate universe, or there could be some other explanation.

Harper apologizes to Rhade for not doing more to help him out, and Rhade reassures him that everything is fine.

Dylan gives Harper a serious chewing-out for insisting on activating the bridge. He indicates that he does not know if he can trust Harper in the future, that he cannot just let him off the hook, and that this is "strike two". After Harper leaves, Dylan admits to Rommie that there was no "strike one", but putting a little extra pressure on Harper will make him work better.