Kirk arrives on Earth for Gary Mitchell’s memorial service, and has the job of informing Gary’s parents about how he died. Kirk’s mind wanders back to another incident, this time aboard the Enterprise on one of the early missions under his captaincy. The Enterprise is ordered back to the planet where Kirk and Gary had previously seen the Klingon ship while they had been serving aboard the Constitution. They are taking a team to the planet which includes Admiral Mangione and Kirk’s old girl-friend, Phelana, among others. The Enterprise crew are initially kept in the dark about the team’s mission, but after the team is attacked by Klingons on the planet, the story gets out. The planet has been used as a prison planet for a group of genetically enhanced Klingons (known as the M’tachtar, with ridged foreheads) who had years ago planned to attack the Federation, but who had been thwarted after the Klingon Emperor had revealed their plans to the Federation (because he feared also for the Klingon Empire). The enhanced Klingons take over the Enterprise, abandoning Captain Kirk and half his crew on the planet, and set off for the Klingon homeworld. Kirk manages to get assistance from a Klingon ship in orbit of the planet, and they catch up with the Enterprise, board it, and take it back before the captain of the Klingon ship gets around to destroying it. The surviving M’tachtar are taken back to the Klingon Empire where they face execution, but the Klingon captain, Kang, considers what the Klingons might do if the genetic transformation could be adjusted so that the resulting Klingons were more under control than the M’tachtar were. At the same time as the Enterprise is at Earth for Gary’s funeral, Dr. Piper leaves and McCoy, Rand and Uhura join the crew, and Sulu becomes helmsman.
It is the year 2329 and Spock is bonded with Saavik. Later, in year 2344, Spock gets a message from Charvanek, the Romulan Commander that he had previously stolen the cloaking device from, implying that there was trouble in the Romulan Empire that was going to affect the Federation. After making further enquiries, Spock goes to Romulus undercover, and meets with Charvanek. Saavik is informed by Uhura of Spock’s unofficial trip, and she also goes to Romulus to try to get Spock out, but then finds that she is in the early stages of pon farr, and the two of them grow increasingly affected by it. They discover that the unpopular praetor, Dralath, is planning an attack on the defenseless Klingon colony world, Narenda III, and the fleet is already underway (they plan to go on from there to attack a Federation colony). Saavik leaves aboard her shuttle to warn the Federation, and Charvanek takes her ship, Honor Blade, to intercept the Romulan fleet. She manages to destroy 3 of the 7 ships in the fleet, but her own ship is disabled. Saavik’s warning gets the Enterprise-C sent to Narenda III, where it is destroyed, but not until most of the rest of the Romulan fleet is destroyed. Charvanek is taken captive by the commander of the fleet, Volskiar, and they return to Romulus. Meanwhile Pardek, the leader of the opposition to Praetor Dralath has been taken captive, and Spock leads his supporters on a mission to rescue him. Commander Tal also meets Spock, and they get enough information against the praetor, then they interrupt one of the praetor’s broadcasts and inform the population of his dishonor. This causes a popular uprising to begin, and the praetor is overthrown, but he escapes. Spock makes his escape from Romulus, assisted by Ruanek, and the two are rescued by Jean-Luc Picard aboard the Stargazer (Stardate 21191.0), which is then attacked in a suicide mission by the ex-praetor, but Dralath’s ship gets destroyed.
The Enterprise rescues the remaining crew of the 21st century, sub-warp (relativistic) colony ship, the Hawking, which is malfunctioning. They also discover that the planetary system that the ship had originally set out for is one that was destroyed by the Doomsday weapon that the Enterprise had destroyed. However, a new home is found for them on the planet Merope IV, which already has a colony but is in need of additional colonists. One group of Merope IV’s colonists mysteriously disappear (just after the Enterprise delivers the Hawking survivors), apparently attacked by a green mossy mass that appeared from cracks in the surface of the planet. The town of Shaku, where the Hawking survivors have been placed and where the leader of the original colonists is, then comes under attack from the green mass, and the Hawking survivors lead an attack on the approaching mass. The attack is unsuccessful, and a number of the Hawking survivors are believed lost. The Enterprise is damaged when it tries to attack the green mass. Later, Spock discovers a partially shielded energy source near where the first colony was attacked, and he believes it may be the “control center” or “brain” of the green mass. He beams down alone to try to make contact, and succeeds in reaching a deal with the creature. It had apparently felt threatened when the colonists moved close to the center of its neural net, but none of the colonists or the Hawking survivors had been killed. They had been held in some form of suspension, and are returned alive as part of the deal. The Hawking survivors decide to stay, and have their old ship destroyed and sent into the system’s sun, burning their bridges behind them.