The death of the USS Enterprise. I never cry, but I came extremely close when I saw this.
More shocks are in store - Admiral Morrow declares that the Enterprise will not be refitted and repaired, but instead will be scrapped. Scotty is assigned as captain of engineering on the new USS Excelsior, while Kirk and the others are left in limbo. During their trip back Genesis has become a galactic controversy, with the Klingons accusing the Federation of developing a super weapon and Kirk of being a murderer.
Back home, Kirk receives a visit from Ambassador Sarek. The Vulcan demands to know why Kirk abandoned Spock on Genesis when he must have been given Spocks "Katra" - essentially his soul. When it's obvious that Kirk doesn't understand, Sarek conducts a mind meld. Apparently Vulcans are able to transfer their consciousness into another via a meld, but it seems that Spock was prevented from doing so by the barrier which separated him from Kirk in his final moments. Kirk, thinking that Spock would have melded with somebody else, checks the visual logs of the Enterprise engine room and sees Spock mind meld with McCoy. McCoy, meanwhile, is gradually beginning to show signs of Spocks personality in his behaviour. He goes to a bar to attempt to hire a ship to take him to Genesis, but a Federation security agent overhears him and arrests the Doctor.
The Klingons are not just complaining about Genesis - one of their spies has procured Carol Marcus's original funding request outlining the devices capabilities, and passes it on to a Klingon Bird of Prey. The vessels Captain murders the witnesses and sets course for Genesis.
At Genesis, the USS Grissom is beginning a survey of the planet. The ship is a small science vessel, with David Marcus - Kirks son - and Lieutenant Saavik on board. David soon detects Spocks burial tube on the surface, and is amazed to detect life form readings down there. He and Saavik beam down to investigate.
Kirk asks Admiral Morrow to let him take the Enterprise back to Genesis to fulfil his promise to see if the effect which created the planet could somehow have revived Spock. Morrow steadfastly refuses, claiming that the Enterprise wouldn't survive another mission. Even when Kirk offers to hire another ship the Admiral remains unmoved. Afterward Kirk informs his friends "the word is no. I am therefore going anyway". They hatch and execute a daring plan to break McCoy out of prison and steal the Enterprise right out of Spacedock, running rings around Starfleet Security and the USS Excelsior in the process, and are soon on the way to Genesis.
When Saavik and David find Spocks burial tube, they discover huge slug like animals all over it - it appears that bacteria on the tube have mutated and grown. When they open the tube a shock is in store - Spocks body is gone. They detect another lifesign nearby and head off in pursuit, soon finding a small Vulcan boy. The Genesis effect has regenerated Spock as a rapidly ageing child. As they report their finding to an incredulous Captain, the Grissom is engaged by the arriving Bird of Prey and destroyed. A Klingon landing party beams down to hunt for Saavik and David, who go on the run with Spock. They manage to elude capture for a day or so, but are eventually run down. While they are interrogated the Enterprise arrives in orbit, and the Klingon Captain beams up to deal with the new threat. He plans a surprise attack on the ship using the cloaking device, but Kirk is a step ahead - he spots a slight visual distortion of the stars and targets it with photon torpedoes, firing the instant the Klingon Captain decloaks.
But things don't go Kirks way. The automation system is not up to handling the ship in a battle, and when the Klingon ship gets a shot off the system shorts out completely. Kirk tries to bluff the Klingon Captain into surrender, but instead the man orders one of the hostages on the planet killed. After a brief struggle the Klingon guard murders David. Stunned by the loss of his son, Kirk invites the Klingons to beam aboard and take control of the Enterprise - and sets the autodestruct sequence before beaming down to the planet. The Enterprise explodes into flames with almost the entire Klingon crew still aboard before crashing into the Genesis planet.
On the planet, things are not going well. David used unstable protomatter in the Genesis Device, and like Spock the planet is ageing rapidly as a result. The only way for Kirk and co. to escape is via the Bird of Prey in orbit. Kirk kills the Klingon guard on the surface and taunts the Captain over a comm channel, hoping to overpower him after he beams down. The Klingon arrives with a weapon pointing at Kirk; he orders most of the others beamed up, leaving only Spock behind. As the planet begins to disintegrate the Captain loses his weapon, and he and Kirk fight hand to hand. Kirk is successful in killing the Klingon, and imitates his voice on the comm device to get the last remaining member of his crew to beam him and Spock aboard. Quickly gaining control of the ship, Kirk heads out of orbit just as the Genesis planet finally breaks apart. Once clear of the planet Spock stops ageing, and they head off to a rendezvous on Vulcan.
Once on Vulcan they take McCoy and Spocks body to Mount Seleya, where a Vulcan high priestess uses a mind meld to remove Spocks Katra from McCoys mind and place it into his body. At first, the new Spock seems not to have any memories of his old life or friends - but when Kirk prompts him, he begins to show signs of recognition and his friends gather around him joyously.
But the crowning glory of the film has to be the sequence leading up to the death of the Enterprise. In the space of a few minutes we get Kirks initial victory over the Klingon, the reversal which leaves the Enterprise crippled, the death of David, and then Kirks ultimate sacrifice. This is some of the strongest stuff we have ever seen in a Trek film or episode - Kirk stands Godlike over Trek in the minds of the fans, and to see him crumple to the floor at Davids death is a moving moment which Shatner plays to perfection. As for the self destruct sequence itself, the Enterprise has always been more than just a ship to Trek fans. She is a character in the minds of the fans, and seeing her torn apart is a sad and horrific spectacle.
The scenes on Vulcan are also powerful - I've always loved the sense of mystery and Alienness which surrounded our glimpses of Vulcan society in episodes like "Amok Time", and this film takes that feeling to another level.
There are relatively few negative points to the film as such. The special effects are sometimes a little less than effective, although the death of the Enterprise is gorgeous. The bar scene is a little unconvincing - the costumes look fairly cheap and tacky and this just doesn't look like the kind of place that would be a regular haunt for either Spock or McCoy. Admiral Morrows insistence that Kirk should not go to Genesis also doesn't quite ring true - Spocks family are very important in the Federation, so much so that it got Kirk out of a court martial in "Amok Time". Surely Sarek would have the influence to get a request like this granted? Yet Morrow dismisses the whole idea out of hand, openly sceptical of "Vulcan mysticism".
The films greatest flaw is that it is ultimately just an excuse to get Spock back alive again. You know this going into it, so much of the impact of the story is diluted. But within this framework the story is adequate, Nimoy does a good job directing and the cast all put in good performances.