The Shechenag start to establish a satellite system around the planet, creating an impenetrable forcefield. While the Shechenag are on the other side of the planet, Spock is able to reflect a force off of some of the satellites, so that the Janus Gate sucks the energy supplies from some satellites, opening a gap. Spock flies a shuttle down through the gap, taking the two Sulus and Chekovs with him, along with a few other crewmembers. Uhura is left in charge on the Enterprise. Meanwhile, Kirk (who calls himself Captain Forester) and his father, George Kirk, have remained behind on Grex (after the rest of the Federation personnel had evacuated) to search for the missing 14-year-old Kirk. The older Sulu and Chekov volunteer to go to Grex to assist the young Kirk in locating his father, and Spock plans to use Security Chief Giotto to maintain the link between Tlaoli and Grex, but the whole team, including Giotto, gets fully transferred to Grex. Captain and Commander Kirk manage to meet up with the group, but Spock now has no one to act as a link between Tlaoli and Grex to bring Kirk back. However, the elder Chekov, knowing that both he and the elder Sulu would vanish if the timeline were corrected, had told Spock of his backup plan, which he now implements by shooting and killing the older Sulu, allowing the younger Sulu to act as the link across time and space and bring Kirk, and Commander Giotto back, and restoring the timeline to at least close to what it had been. As the Enterprise moves back out of the three days it had relived after the dramatic escape from Psi 2000, their memory of the events at Tlaoli fades.
Kirk is getting frustrated with teaching at the Academy, but then he is approached by his two nephews, Julius and Alex, who want him to join them in establishing a colony on the uninhabited planet, to be called Sanctuary. He is initially going to refuse, but when he is assigned to oversee the over-emotional Skalli (a Huanni) he decides to join them, and gets Scotty and Chekov involved as well (and later finds that Skalli, who is from a nearby planetary system, has also joined the colonists). The trip to Sanctuary is uneventful, and the colony is being established. When communications difficulties start to occur, Kirk discovers that the problems originate from a previously unknown facility run by the Falorians, who Julius had negotiated with to obtain the use of the planet for the colony. The Falorians claim it is a trading post, but Kirk and his team discover that it is a research facility, apparently planning some form of attack on the Federation. After Kirk and his team break into the facility, the colonists’ ship gets destroyed and they are stranded and unable to communicate with the outside. However, the Klingon Chancellor, Azetbur, had sent a cloaked warbird to follow and protect Kirk (as a debt of honor for his work after their moon was destroyed) and they get word back. Azetbur gets Spock, Uhura and McCoy the use of another Klingon ship to go and investigate what is going on. It turns out that the Falorians used to be slaves of the Huanni, and had been deposited on their current planet, Falor, when their usefulness to the Huanni had expired. Their previous work in the dilithium mines had led them to a plan to infect the Federation with a nanotechnology virus that, when activated, would render all dilithium useless. They don’t realize that the impurities in the Federation’s dilithium would result in warp core breaches if the virus was activated. Along with their Orion allies, they plan to invade and re-take Huan, while holding the Federation at bay with the threat of activating the virus. Kirk gets the colonists into hiding (although some, including Alex, get captured) and he and his team (including Julius) invade the Falorians’ base. With the help of Spock and the Klingons, they take the base and capture the leader, Lissan (who later gets killed by the Orions after deactivating the virus). Sulu, aboard the Excelsior, gets the help of the Orions to stop the Falorians’ attack on Huan, after convincing the Orion’s leader that the Falorians were planning to double-cross them. After all that, Kirk returns to Earth, and is looking forwarded to being at the launching ceremony of Captain Harriman’s Enterprise.