It's the last day of the 5YM. The Enterprise has been ordered home and the whole crew is looking forward to several months’ worth of accumulated leave time. At the same time they're pondering where their careers will go now that this mission is over. Most of the senior officers have been offered teaching assignments, to better prepare the next generation of Starfleet officers for what they'll be facing out there.
Spock has been offered a position at the Vulcan Science Academy, with McCoy and Scotty being offered senior positions at Starfleet's schools of Medicine and Engineering respectively; Kirk, still being young for his rank, fully expects to serve another tour of duty as a starship commander preferably aboard the Enterprise, but there are rumors that Starfleet may have something else in mind.
The junior officers are all expecting promotions and new assignments elsewhere, for them the happiness is mixed with sadness at the inevitable parting of the ways. Sulu is being considered for an Executive Officer's slot aboard the Lafayette, Kirk has nominated Uhura for Command School, Chekov has put in a request for Security and Intelligence training, and Chapel is considering leaving nursing behind and becoming an MD.
Only a day out from Earth, the Enterprise encounters the First Federation starship Fesarius. The vessel seems to be a derelict drifting in space with most of her nodes dark. Kirk leads a boarding party and finds Balok in his quarters near death. He tells the tale of how the Fesarius encountered an alien vessel adrift, he sent young Mr. Bailey to render aid but somehow he was overcome and instead led the aliens back to the Fesarius intent upon capturing the massive vessel. Balok managed to keep them from acquiring the main ship by sabotaging his own vessel but they were able to seize the small pilot vessel instead. Balok jury rigged the engines and headed for Earth but the repairs failed and he has been drifting for several days. When asked why he headed for Earth Balok explains that Bailey had announced that he intended to teach Starfleet a lesson for abandoning him. Bailey had been growing more dissatisfied with his posting to the Fesarius for some months and contact with the aliens seems to have somehow brought his resent out in full force. After saying this, Balok dies.
Kirk and the boarding party return to the Enterprise. Uhura reports that she’s picking up a series of distress calls from ships and installations the renegade pilot vessel has attacked which Spock analyzes to figure out a pattern to Bailey’s actions. He determines that Bailey is most likely to strike next at Alpha Centuari with a 87.936 percent probability of following it up with a strike at Earth itself. Captain Kirk contacts Starfleet with their conclusions and is ordered to Alpha Centauri at maximum warp, the Earth Sector Patrol Group will meet him there. Kirk, however, has a gut feeling that Bailey has tapped into the communication and will therefore head straight to Earth. Rather than risk alerting Bailey, Kirk ignores his orders and directs the Enterprise to Earth at warp 7.
Kirk’s guess is right, Bailey and the pilot vessel have just begun attacking Earth installations when the Enterprise arrives. The starship attacks but the pilot vessel is every bit as tough as Balok had stated years earlier. Between the Enterprise’s superb crew and his greater tactical skill, Kirk manages to avoid crippling damage but it is clear that the pilot vessel is more than a match for the Enterprise. Kirk tries to talk Bailey into giving up this senseless quest for revenge, but Bailey goes on and on about how Earth will suffer as he has. During his tirade, Spock notices something strange in a corner of the pilot vessel’s bridge. Enhancing the image he finds it to be one of the flying parasites thought to have been eradicated on Deneva. Obviously Bailey was infected when he went aboard the derelict alien vessel, the creature must have discovered Bailey’s dissatisfaction with his assignment and expanded upon it until Bailey had become a willing tool in the creature’s quest for revenge.
With this information in his hands Kirk formulates a plan. The Enterprise launches a full scale attack intent on collapsing the pilot vessel’s deflectors. In spite of the Enterprise taking severe damage he perseveres and manages to burn through the shields. At this point Scotty beams a dozen high-powered ultraviolet lamps aboard the pilot vessel killing most of the creatures. Lieutenant Commander Giotto and his security teams follow up with hand-held lamps and finish the job. Back in his right mind Bailey is appalled at the death and destruction that he has caused and breaks down in tears.
The badly battered Enterprise enters Spacedock where a hero’s reception awaits them. Starfleet decides that the ship is too badly damaged to go through merely a routine refit. Instead she will be the test vessel for a major upgrade program. They tap Scotty to oversee the program. Captain Kirk is offered a promotion to Admiral and a position on the commanding admiral’s staff, he says he’ll consider it and make his decision when he comes back from leave. Spock decides to return to Vulcan, for a time at least. McCoy has yet to accept his teaching position but figures he probably will. The three friends share a drink together in a small lounge overlooking the Enterprise. McCoy asks if they’ll ever be serving together again. Kirk remarks that it’s a small galaxy. Spock states that while this may be true in cosmic terms, in real terms the galaxy is… McCoy interrupts him asking if he has to be so literal all the time? Spock raises an eyebrow at him as Kirk looks on smiling then says – Yes, Bones, I’m sure we’ll be together again, there’s a whole lot more galaxy waiting to be explored. Then the camera pans over to the Enterprise as a new slower-paced voice over of the opening monologue plays, then fade to black and roll credits.
