Absolute quiet. Sound bleeds in. Low level background noises of Enterprise bridge, clicking of relays, minor electronic effects. A female Vulcan sits in the command chair on the bridge of the U.S.S. Enterprise. We see the crew at stations; (screens and visual displays are in use): Commander Sulu at the helm, Commander Uhura at the Comm Console, Dr. Bones McCoy, and Spock at his post. The Captain is new -- and unexpected.
Lt. Saavik (Kirstie Alley) is young and beautiful. She is half Vulcan and half Romulan. In appearance she is Vulcan with pointed ears, but her skin is fair and she has none of the expressionless facial immobility of a Vulcan. While the senior crew and some cadets work at their consoles, Saavik, makes a log entry, then orders Commander Sulu (George Takei) to project a course to avoid entering the Neutral Zone at the Klingon frontier.
Suddenly, Uhura (Nichelle Nichols) receives a distress call, minimal signal. Saavik requests to amplify as Sulu projects a course change. Uhura confirms it is an emergency distress call from the Kobayashi Maru inside the Neutral Zone. A ship nineteen periods out of Altair VI that has struck a gravitic mine, many casualties, and have lost all power.
Uhura requests their coordinates, but the message is breaking up and they gather only partial information. The vessel, located in Gamma Hydra - Section Ten, is a third class neutronic fuel carrier, crew of eighty-one, three hundred passengers. The hull is penetrated and life support systems are failing. Tactical appears on the big screen displaying data on the Kobayashi Maru.
Despite warnings from both Sulu and Spock (Leonard Nimoy), Saavik orders Sulu to plot an intercept course and enter the Zone in order to beam the survivors aboard. Enterprise approaches the stricken vessel. Saavik orders the transporter room to standby and be ready to beam the survivors aboard. Uhura reports she has lost their signal and the computer voice announces that sensors indicate three Klingon Cruisers, bearing 316, mark 4, are closing fast.
On screen we see the approach of the Klingon vessels, they are dark and sinister. Saavik orders battle stations and shields activated, the alarm sounds off. Uhura attempts to inform the Klingons they are on a rescue mission, but they're jamming all frequencies. The Klingons are on attack course and closing. Saavik makes an agonized choice and orders Sulu to get the Enterprise out of there. The Klingon cruisers are now approaching, bearing 090, mark 20.
The Klingons fire photon torpedoes. Saavik orders evasive action. Sulu does his best, but Enterprise is hit; Sulu is hurled from his station, and Bones hurries to him. Scotty reports the Main energizer was hit. Saavik orders him to engage auxiliary power and prepare to return fire. The bridge takes another hit -- a big one. In its wake there is a second electrical explosion along the communications panel. Uhura falls from her station. Bones rushes to her side amid the smoke and alarms.
A Cadet reports shields are collapsing and Scotty announces they are losing auxiliary power. Saavik orders the crew to fire all phasers, but Spock reports there is no power to the weapons system. Another hit: reverberating flashes of spark and flame on the bridge. Spock dies. Bones comes to him, but even as he coughs his way through the smoke, a final hit and Bones falls. The room is smoke filled and a shambles. Saavik looks about in shock.
The Enterprise is heavily damaged; many of the bridge officers are killed. Scotty reports they are dead in space. Saavik digests this for a painful moment. Then, touching a comm button, she orders the activation of the escape pods and send out the Log Buoy, they must abandon ship.
Then the filtered voice of Admiral Kirk (William Shatner) is heard. The bridge viewscreen slides aside, revealing a lighted room beyond. The Kobayashi Maru was a Starfleet Academy test, one Saavik does not believe to have been a fair test of her abilities.
Kirk explains that the no-win scenario is a situation every commander may face, and that how one faces death is equally important as how one faces life. Saavik seems ruffled at the advice, but Kirk offers that now she has "something new to think about."
As he leaves, McCoy asks Kirk why the Enterprise will not receive an experienced crew. Kirk replies that space exploration should be left to younger crews, a remark that puzzles Uhura.
Outside the simulator room, Spock awaits Kirk's opinion of the cadets' performance. Kirk notes that the trainees wreaked havoc with the simulator room and Spock alike. Spock recalls Kirk's own Kobayashi Maru, noting that Kirk himself took the test three times and that his final solution was "unique." Kirk then thanks Spock for his birthday present, an antique copy of Charles Dicken's "A Tale of Two Cities." Spock then leaves on a shuttlecraft to board the Enterprise and await Kirk's arrival--he will later inspect the ship.
Kirk then retreats to his apartment, to be greeted by Dr. Leonard McCoy (DeForest Kelley), who presents him with two gifts; a bottle of finely-aged Romulan ale and a pair of antique eyeglasses. Noticing Kirk is going through a mid-life crisis, he questions whether Kirk really wants to carry on the duties of an admiral, or to be "galaxy hopping" in a starship.
McCoy urges Kirk to get back his starship command, and the two share a drink sitting by the fireplace. Meanwhile, Commander Chekov (Walter Koenig) is on board the U.S.S. Reliant, which is orbiting the planet Ceti Alpha VI. The crew is searching for a lifeless planet to satisfy the requirements of a test site for the "Project Genesis" experiment, a terraforming program proposed to the Federation by a group of scientists.
Although Ceti Alpha VI should be incapable of supporting life, Chekov detects a minor energy reading on a scanning device. Chekov and Captain Terrell (Paul Winfield) beam down to the surface to investigate. Upon arrival, they fight their way through a blinding sandstorm until they discover and enter what appears to be a crashed derelict vessel. They soon discover that the derelict is actually cargo containers assembled together from the S.S. Botany Bay, a ship Chekov remembers all too well.