On the eve of retirement, Captain James T. Kirk is asked to come back for one more assignment; which is to escort the Klingon ambassador through federation space, so both sides can finally become allies. Although Kirk is extremely reluctant at first, he finds that he has little to no say in the matter, so he proceeds in the mission.

However, through a series of events, Kirk and McCoy are framed for the murder of the Klingon ambassador, and uncover an elaborate conspiracy in the works to destroy the federation's last hope for peace.

Admiral Kirk and his fugitive crew must return to the federation, to face the crimes they committed in the previous movie. However, when a mysterious alien probe comes that could wipe out the federation, Spock deduces the only species capable of communicating with it are the long since extinct humpback whales.

Therefore, Kirk orders his crew to go back in time to the 20th century, in order to get the whales of the past, to save their future.