Starfleet loses contact with NCC 1764 U.S.S. Defiant and the Enterprise is despatched to investigate her last reported location, which is in an uncharted area of the galaxy. The vessel's engines start to lose power and ship's sensors indicate a nearby fracture in the fabric of normal space that seems to be the cause of the power drain. The Defiant is sighted, glowing strangely, and a boarding party consisting of Kirk, Spock, Chekov and McCoy beam over in environment suits to find that her entire crew appears to have killed each other.

The solidity of the Defiant starts to waver and everyone is beamed back aboard the Enterprise safely except for Kirk who is caught in a spatial interphase between two universes. On board the Enterprise the crew starts to suffer the effects of the interphase and begins to exhibit the same murderous tendencies that must have affected the Defiant's crew. An alien craft approaches the Enterprise, announcing that it is a Tholian vessel under the command of Loskene and demanding that the Federation ship leaves their area of space within two hours.

An unsuccessful attempt to retrieve Kirk is made during the next interphase and the time limit passes, after which the Tholian vessel attacks. The Enterprise returns the enemy fire and manages to repulse the attack but leaves itself dangerously low on power. A second Tholian vessel arrives on the scene, docking with the first. When they separate, a bright strand is created between them and they manoeuvre around the Enterprise weaving a web-like energy field that threatens to enclose the ship.

Thinking that they have lost Kirk, Spock and McCoy listen to a recording the captain has left to be opened in the event of his death in which he exhorts them to use their different points of view to support and help each other. McCoy eventually finds an antidote to the effects of the interphase by using a diluted form of the deadly Klingon nerve gas Theragen. Strange, ghost-like sightings of Kirk are reported around the ship but these are put down to hallucinations until Kirk appears in front of the bridge crew.

With the Tholian energy web virtually complete, Spock orders the transporter to be locked on to Kirk's 'ghost' and then uses all the ship's power in a last moment effort to break free of the Tholian web. Kirk is successfully retrieved from the interphase and the Enterprise leaves Tholian space. Kirk is keen to discover what happened aboard while he was 'away' and is amused by Spock's and McCoy's insistence that they worked perfectly well together and did not have time to open his 'last orders'.