After three days of studying an uncharted area, an object moving at light speed suddenly approaches the USS Enterprise. Spock orders evasive maneuvers, but the deflectors prove ineffective. Alerted to the situation, Spock signals the alarm, only to quickly retract it when the object decelerates. Lieutenant Dave Bailey, the chief navigator, is visibly shaken. Unable to dodge the impending danger, Lieutenant Sulu declares a red alert and requests the captain to the bridge.

The captain's log recorded Stardate 1512.2, marking the third day of a star mapping mission. Then, suddenly, an unknown cube-shaped object blocked the ship, prompting Mr. Spock to sound a general alert. As for the captain, he was in sick bay taking care of his routine medical check.

As the red alert blared through the ship, Doctor McCoy remained in sickbay, dutifully recording Kirk's medical information on a PADD. The captain scolded McCoy for not alerting him to the alert, to which McCoy retorted happily, "What am I, a doctor or a shuttle conductor? If I responded to every light that flashes around here, I'd be talking to myself!" With that, Kirk left McCoy alone in the sick bay.

As Bailey attempted to interject Spock's words on the bridge, he justified his emotional response earlier by mentioning his adrenaline gland. Spock sarcastically inquired if Bailey had considered taking it out, and Sulu jokingly warned of the dangers of going head-to-head with Spock. The team examined the item and concluded it was solid, 107 meters on each side and nearly 11,000 metric tons in weight. Scott was puzzled by what powered it and enabled it to sense and respond to the movements of the Enterprise. McCoy had no report either. All attempts to speak with it were unsuccessful. Finally, Bailey suggested they use phasers weapons, to which Kirk sternly replied, "this isn't a democracy, Mr. Bailey."

The captain reported that their star charts did not show any nearby habitable planets, and the origin and goal of the cube remained a mystery. The cube had stuck them in place for eighteen hours. Later, the top officers met in the briefing room. Spock hypothesized that the object could be a buoy or something to trap them. Kirk and Spock agreed that lingering longer would imply a lack of strength. Nevertheless, Bailey believed they were meant to ready their phasers and ordered the phaser crew to take action. When overruled, he attempted to justify his decision.

Kirk commands Bailey to navigate a curved route far away from the object. Following his instructions, the ship accelerates from 0.25 to 3 warp speed, yet the thing remains near the Enterprise, emitting dangerous radiation and rapidly approaching. When it is 51 meters away, Kirk orders Bailey to fire the main phasers. After a brief moment of hesitation, Kirk reaffirms his command, and the blast obliterates the object. The shockwave from the explosion rocks the Enterprise.

Captain's Log, Stardate 1514.0 the captain entered into the log that the cube had been demolished, and the vessel had only sustained minor damages. Spock found that the sensors weren't detecting any other objects and theorized that it would come across intelligence that was likely dissimilar and better than themselves if the ship pushed on. Kirk decided to move forward since their mission was to make contact with extraterrestrial life. He ordered the phaser crew and engineering to do some exercises, as he found their response to the attack was too slow. Bailey was appointed to oversee the drills.

As the crew was exhausted, McCoy queried Kirk's decision to appoint Bailey as navigator, feeling that he had been elevated too quickly. During the crisis, Bailey had been slow to comply, and Sulu had to intervene. McCoy further suggested that Bailey's emotionalism on the intercom during the drills told he wasn't up to the task, but Kirk disregarded the doctor's concerns.

Kirk and McCoy keep talking in Kirk's cabin while having a drink. Spock informs him the last drill has yielded a score of 94%, but Kirk insists they reach 100%. He is further vexed by McCoy putting him on a salad regimen to lose weight and someone giving him an attractive female yeoman, Janice Rand, who just brought the salad.

Kirk and McCoy stop to hear the intercom, where Bailey commands a second drill. However, Sulu revokes the order because a brand-new object is on a course toward them. It is round and much larger than the original, measuring a mile in diameter. Sulu declares that "this is not a drill," and Kirk immediately leaves his salad and sprints to the bridge.

When the object appears on the viewscreen, Kirk reduces speed to warp 2. A powerful tractor beam grabs the Enterprise, and the engines begin to overload. Kirk orders a halt and the phaser crews to prepare. He tells Bailey to reduce the primary viewscreen magnification, but when Bailey doesn't respond, Sulu does it instead. Kirk requests Uhura to open a communication channel and begins to speak, but Bailey notices a message on the navigation beam.

Balok asserted that the Enterprise and its personnel had demonstrated their hostile intent by disregarding the cube, a warning buoy, and even destroying it. Consequently, the Fesarius were now assessing their "fate." When Kirk attempted to explain the situation to Balok, robust sensors penetrated all Enterprise systems. Balok refused to accept any further communication from the Enterprise and warned that he would eradicate them if they made any move. When Kirk sent out a recorder marker, Balok annihilated it and declared that the Enterprise must be destroyed, granting the crew ten minutes for their last rites, assuming they had "a god or gods." When McCoy informed Kirk that Balok's message had been broadcast throughout the ship, Kirk addressed his crew with a calming and optimistic note.

Upon first encountering the Enterprise crew, Balok signals to the Fesarius that they should retrace their steps, but all their engines and weapons are rendered powerless. Spock, driven by his inquisitive nature, gets a glimpse of Balok's intimidating visage, who then declares that the Enterprise has no chance of fleeing.

Bailey's terror escalated as he comprehended his inevitable demise, prompting him to unleash a rant against the bridge officers for their aloofness and seeming indifference in the face of their destruction. Kirk commanded that Bailey be relieved of duty and that Dr. McCoy show him to his chambers. Dressed by the situation's grimness, Kirk begged Balok to believe their peaceful objectives, yet Balok disregarded him.

With only a few minutes to spare before the disaster, Kirk asked Spock for possibilities, but Spock responded that it was too late, like a game of chess that had been lost. "Checkmate," Spock concluded. Kirk refused to accept this, and Spock almost apologized, but he quickly corrected himself by insisting he didn't have a better plan. McCoy used the pause to suggest recording the incident with Bailey as fatigue, but Kirk denied this. Instead, McCoy argued that it was due to Kirk's heavy demands on the young navigator, and he threatened to challenge Kirk in his report. "I'll point out that I warned you of Bailey's condition. That isn't a lie!" Kirk furiously called him out, but then a moment of inspiration hit him.

With no chess in his arsenal, Kirk turns to poker and mentions corbomite, a mysterious material aboard all Starfleet ships. He explains that the Enterprise is equipped with a defense mechanism - if any destructive force comes into contact with the ship, the corbomite triggers a reaction that results in the attacker's destruction. Over the past two centuries, no vessel attacking the Enterprise has survived. Kirk dares Balok to open fire, but nothing happens. As they prepare to meet their demise, Bailey returns to the bridge and requests permission to resume his duties, which Kirk affords him. Seconds away from destruction, Sulu counts down the final moments, but just as the timer reaches zero, the Fesarius doesn't attack. The crew can't believe their luck, and even Spock admits that poker is a compelling game.

Balok hails the Enterprise, and Captain Kirk is ready to either bluff or stands his ground. Balok says that the destruction of the Enterprise has been put off only if they can provide proof of the corbomite device. Kirk refuses, and Balok's small pilot vessel emerges from the Fesarius. He then declares that the crew will be sent to a planet of the First Federation, and the Enterprise will be demolished. He captures the Enterprise using a tractor beam and warns that any escape attempt or attempt to damage his ship will immediately destroy the Starfleet vessel.

The Enterprise has been captured and has not offered any resistance. My goal is to appear compliant. Balok's tractor beam must be depleting a large amount of energy from their small vessel. I'm asking myself, will this leave them vulnerable?

With the Enterprise in tow, Kirk demands a sharp turn, moving away from Balok, aiming to push the tiny ship's engines to their limits against the Enterprise's engines. The impulse engines are activated but quickly begin to overheat. Kirk requests further power to be added. As the pressure intensifies, the Enterprise starts to shake, but Balok's vessel also begins to show signs of stress. Mr. Spock alerts that the engines are about to blow, but Kirk is resolute and orders to increase the thrust against the tractor beam. As the crew endures the terrible ride, Bailey eventually reports that they are escaping. The Enterprise veers away from Balok, whose ship is seemingly disabled.

Scott informs the captain that their engines need urgent attention, while Spock cautions them that Balok has beamed out a desperate plea for help. Uhura succeeds in picking it up, detecting that Balok's engines are down and his life support system is in peril. She assesses that the signal is too weak for the mothership to have received it. Kirk takes the Enterprise on an intercept course for a rescue mission. McCoy is unconvinced, but Kirk stands firm that their mission is to explore alien life, regardless of whether they are friends or foes. He orders McCoy and Bailey to accompany him on the task and leaves Spock aboard the ship in case Balok lures them into a trap. Balok bursts out laughing.

When the trio stepped onto the escort ship (with lowered heads due to the lack of headroom on the extraterrestrial vessel), they discovered that the imposing creature they had seen was, in fact, just a dummy puppet. The genuine Balok welcomed them on board, appearing as a small child, and offered them a glass of tranya as a symbol of goodwill. He went on to clarify that he had utilized the puppet to assess the Enterprise's true aims, as he had suspected that even the ship's records could have been misleading. Furthermore, he revealed that he operated the Fesarius starship single-handedly from his own smaller craft but lamented how lonely this made his journeys. Finally, Balok proposed that one of Kirk's crew remain with him to share knowledge and cultures.

Without hesitation, Bailey offered his assistance, and Kirk accepted, noting that although Bailey may not be the ideal example of Starfleet, the situation would be an excellent opportunity for him to gain knowledge and for Balok to understand more about the frailty of Humans. Amused by the suggestion, Balok concurred with Kirk's rationale and offered to show the trio around his ship while awaiting the Fesarius's return. He then commented on the resemblance between himself and Kirk, noting that they both take immense pride in their vessels.