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The Starship Enterprise is sent to pursue an alien ship that has destroyed a number of Earth Outposts, the latest being #4 near the Romulan Neutral Zone. It is feared that after a century of non-contact the antagonistic Romulans have built up their forces for another round of warfare. Captain Kirk arrives there and discovers the lone ship, identified as a Romulan Bird of Prey, has a surprising ability - it can attain invisibility with a cloaking device.
The Enterprise finds that this cloak is not perfect and manages to track the ship - it is returning home after what appears to have been a test of strength. The Enterprise also taps into the Romulans' internal security camera feed and makes another astonishing discovery: the Romulans are, in appearance, identical to the Vulcans, a member world of the United Federation of Planets. One of the Enterprises' bridge staff, Lieutenant Stiles, has long held a personal grudge against the Romulans for family reasons left pending from the last war. Stiles begins to associate the Vulcan Mr. Spock, a fellow officer, with his grievances.
During a briefing over the Romulan ship's capabilities, Mr. Spock surprises everyone when he counsels the Captain to attack the intruders as a demonstration of strength. While Spock is not positive, he thinks it likely that Romulans are an ancestral off-shoot of the Vulcans. Such an ancient schism would have occurred during an age of savage warfare, before the Vulcan philosophy of logic as introduced by the great Surak, took hold. If these are a people who rejected Surak, then they will imply weakness from their foes if not confronted.
A mutual game of cat-and-mouse between the two ships ensues, with each ship having unique advantages over the other. The Romulan ship has far greater stealth than the Enterprise and is armed with plasma torpedoes of immense destructive power. However, the Enterprise is much faster and more maneuverable than its opponent. The Romulan plasma torpedoes prove much less effective against an evasive target than they were against stationary asteroid bases, and require so much power to fire that the ship must decloak to do so. While cloaked, however, the Enterprise is unable to target the Romulan ship effectively itself.
As this conflict proceeds the episode depicts the activities of both the Enterprise crew and the Romulan ship's captain, revealing the Romulan to be a thoughtful and well-developed character. The battle becomes as much a personal battle of wits between the two captains as a battle between starships, with each attempting to understand the other's psychology.
Finally, it seems to the Romulans that they have the upper hand. They should make for home but they can't resist a finishing shot. When the Romulan ship becomes visible one last time to launch a plasma torpedo, the Enterprise manages to disable it with its phasers. But not before suffering an equipment failure which leaves the weapons system crucially off-line and the bigoted Lieutenant Stiles incapacitated at his post. Ironically it is Mr. Spock who rescues both the ship and Stiles.
Kirk hails the crippled Bird of Prey and at last communicates directly with his Romulan counterpart, offering to take on survivors. The Romulan captain responds that he has "one last duty to perform" and triggers his ship's self-destruct, preventing its crew and technology from falling into Federation hands.