The Enterprise responds to a distress call from the Klingon farming colony on Signi Beta, which is being attacked by unidentified craft. Signi Beta had been contested by the Klingons and the Federation, but, under the terms of the Organian Peace Treaty, had been awarded to the Klingons. Commander Kor also responds to the distress call, and at first attacks the Enterprise, assuming they are the culprits, but soon agrees to cooperate to find the real attacker. Six alien starships approach soon after Federation and Klingon away teams (led by Kirk and Kor) have beamed down, and position themselves in such a way as to prevent the away teams being beamed up. The colonists (lead by Kerdoch) and the away teams suffer through a number of attacks by the aliens, although the attacks appear to be primarily aimed at destroying the Klingon’s crops. In orbit, the Enterprise (later joined by the Farragut) cooperate with Kor’s ship, the Klothos (which is later joined by two other Klingon ships), in trying to eliminate the attack craft launched from the alien vessels (which are also joined by three others that had been hiding behind the planet). Kirk finally gets the aliens to talk, by going out towards their camp half naked. The aliens are known as the Narr, humanoids with a catlike appearance, who wear armor that can only be operated using antigrav units. It turns out that the Narr had been manipulating the plant life on the planet over an extended period, with a view to using it as a source of crops at some future time. Kirk makes a deal with them whereby the Klingons will be allowed to remain on the planet, growing their own and the Narr’s crops (which they will sell to the Narr), while the planet remains officially the property of the aliens. The Klingons learn from the Federation fighting with them, and from the aliens keeping to the terms of the deal, that even their enemies have honor. [Timeline: about a year after Kirk had suggested the best defense was nothing more than smoke and mirrors.]
The Enterprise is on a mission to the rather reclusive colony on Tyrtaeus II, which had had its master database wiped clean by a computer virus. While there, they notice what, at first, appears to be an asteroid, but then it begins to maneuver towards the sun. Along with two Tyrtaeans, Myra Coles and Wellesley Warren, the Enterprise goes to investigate and finds that it is a powered craft, and there are fears that its drive field may cause dangerous effects to the system’s sun when it crashes into it. Efforts to divert the craft fail when the vessel brings itself back to its original heading towards the sun. An away team fails to find any control center, or inhabitants, although life forms are indicated by the tricorders. The away team are also affected in various ways by feelings of unease aboard the vessel, and they give up the attempt to locate inhabitants. Spock returns to the vessel, as he was least affected by the feelings of unease, but then he gets trapped aboard when the vessel accelerates and its energy field interferes with transporter operation. With no other apparent course available, they try to destroy the vessel with photon torpedoes, but they have almost no effect. The vessel, with Spock aboard, enters the sun, but instead of being destroyed, it ends up in a kind of station inside the sun. After locating some form of control panel, Spock discovers that the craft is inhabited by beings that live in a virtual universe generated by the vessel’s computers, which are a form of artificial intelligence. They know of, but do not want contact with, the “real” universe and its inhabitants. Kirk and McCoy use a shuttlecraft to enter the sun through the same portal (or “warp window”) the vessel had used, and after some discussion, the three Enterprise crewmen are allowed to leave the vessel. Soon afterwards, the vessel reemerges from the sun (where it had been recharging its energy supplies), and the Enterprise follows but is unable to keep up with it, as Kirk hoped - he wanted to show the occupants that they need not fear the Federation’s curiosity, because they could always escape from them. [Timeline: Yeoman Janice Rand is still aboard, and not long after the TV episode ‘Court Martial’.]
Just before the Apollo 11 moon landing, Gary Seven receives an emergency call from Agent 146 saying that the Romulans have discovered his (supposedly) secret base, and are planning to change the future by killing Spock at Camp Khitomer (Stardate 9521.6). Using his transporter, Gary Seven, along with Roberta Lincoln and Isis the cat, travel through time and space to request Kirk’s assistance in preventing the potentially disastrous change to the timeline, although Gary Seven is unwilling to say exactly what the problem is. Kirk is unwilling to break away from his current rescue mission, so Gary Seven effectively hijacks the Enterprise through a wormhole, leaving it well inside Romulan space, near Agent 146’s base on a cloaked planet. Kirk decides to investigate the planet, taking Chekov and Sulu with him, and Gary Seven escapes from the brig and joins them on the planet. The away team is then cut off from the Enterprise when the Romulans operate the base’s shields. Spock is under orders to return the Enterprise to Federation space, but Roberta convinces him not to. The away team arrive just after Agent 146 has been killed (year 2269, Stardate 6021.4), and almost, but not quite, manage to stop the Romulan commander, Dellas, from travelling into the future to the Khitomer conference. Consequently, Gary Seven has to follow her and stops her just before she is able to carry out her plan. They transport back to the base just before the place is about to self-destruct, but Isis has escaped aboard the Enterprise and adjusts the transporters so that she can beam the away team and the Romulans aboard, even through the shield. Gary Seven gets the Enterprise back into Federation space in time to carry out its rescue mission, and Spock uses the mindmeld technique to make those involved forget their knowledge of the future. [Timeline of main action: Stardate 6021.4, about a week after the incident with Dr. Lester, where Kirk ended up in a woman’s body, less than a year since the Romulans and the Klingons had formed an alliance, and two years after the mission to Organia.]