In 2286, an enormous cylindrical probe moves through space, sending out an indecipherable signal and disabling the power of every ship it passes. As it takes up orbit around Earth, its signal disables the global power grid and generates planetary storms, creating catastrophic, sun-blocking cloud cover. Starfleet Command sends out a planetary distress call and warns all space-faring vessels not to approach Earth.
On the planet Vulcan, the former officers of the late USS Enterprise are living in exile after the events of Star Trek III: The Search for Spock. Accompanied by the Vulcan Spock, still recovering from his resurrection, the crew take their captured Klingon Bird of Prey (renamed the Bounty, after the Royal Navy ship) and return to Earth to face trial for their actions. Receiving Starfleet’s warning, Spock determines that the probe’s signal matches the song of extinct humpback whales, and that the object will continue to wreak havoc until its call is answered. The crew uses their ship to travel back in time via a slingshot maneuver around the Sun, planning to return with a whale to answer the alien signal.
Arriving in 1986, the crew finds their ship’s power drained by the time travel maneuver. Hiding the Bounty in San Francisco’s Golden Gate Park using its cloaking device, the crew split up to accomplish several tasks: Admiral James T. Kirk and Spock attempt to locate humpback whales, while Montgomery Scott, Leonard McCoy, and Hikaru Sulu construct a tank to hold the whales they need for a return to the 23rd century. Uhura and Pavel Chekov are tasked to find a nuclear reactor, whose energy leakage can be collected and used to re-power the Klingon vessel.
Kirk and Spock discover a pair of Humpback whales in the care of Dr. Gillian Taylor at a Sausalito aquarium, and learn they will soon be released into the wild. Kirk tells her of his mission and asks for the tracking frequency for the whales, but she refuses to cooperate. Meanwhile, Scott and McCoy trade the formula of transparent aluminium for the materials needed for the whale tank, while Sulu secures the use of a “Huey” helicopter to transport them. Uhura and Chekov locate a nuclear powered ship, the aircraft carrier Enterprise. They collect the power they need, but are discovered on board. Uhura is beamed out but Chekov is captured, and subsequently severely injured in an escape attempt.
Gillian learns the whales have been released early, and goes to Kirk for assistance. Gillian, Kirk, and McCoy rescue Chekov from a nearby hospital and return to the now recharged Bird of Prey. After saving the whales from whalers and transporting them aboard, the crew returns with Gillian to their own time. On approaching Earth, the Bounty loses power due to the alien probe, and crash-lands into the waters of San Francisco Bay. Once released from near-drowning, the whales respond to the probe’s signal, causing the object to reverse its effects on Earth and return to the depths of space.
Later, the Enterprise crew stand judgment before the Federation Council. The Council acknowledges their part in saving the planet and drops all charges, save one against Kirk for disobeying a superior officer. Kirk is demoted to the rank of Captain and returned to the command of a starship. Kirk and Gillian part ways, as she has been assigned to a science vessel by Starfleet, while Spock’s father Sarek finally accepts his son’s earlier choice to enter Starfleet. The crew discovers they have been awarded the newly christened USS Enterprise (NCC-1701-A), and leaves on a shakedown mission.
Star Trek Command 