The story opens with an immense explosion somewhere in space. Huge shockwaves radiate out from the blast site. On board the USS Excelsior, Captain Ikaru Sulu makes an official entry in his log, noting that his mission of "cataloging gaseous anomalies in Beta Quadrant" is over and they are returning to Earth. The ship is suddenly struck by one of the shockwaves from the explosion. Sulu orders his crew to restore control to the ship, which is done quickly.
Looking over their scanning equipment, the crew determines that the shockwave originated at the location of the Klingon moon Praxis. Sulu remarks that Praxis is the primary source of energy for the Klingon Empire, and orders a message be sent stating he and his crew will assist if necessary. They receive an emergency transmission from Praxis showing a Klingon worker consumed in flames.
A second message comes from Brigadier General Kerla that acknowledges the explosion (he calls it "an incident") and that they do not require assistance from the Federation. He also commands them to stay out of the Neutral Zone. When one of the crew asks if they should report the incident, Sulu replies "Are you kidding??"
On Earth, Captain James Kirk, Dr Leonard McCoy and Engineer Montgomery Scott attend a top-level meeting of Starfleet. They are told almost immediately that the Klingon Empire "has roughly 50 years of life" remaining. Charge of the meeting is turned over to the Federation's special envoy, Captain Spock. He tells the committee that the explosion of Praxis two months earlier has caused an environmental catastrophe on the Klingon homeworld of Q'ono'S (Kronos). Pollution of the planet's ozone layer has left Klingon civilization with only 50 Earth years of oxygen.
The Klingon Empire, due to its enormous military budget, is unable to reverse the devastation and has turned to the Federation for assistance. However, as Spock notes, assistance cannot begin until a treaty has been negotiated with the Federation of Planets to cease all hostilities between the two. Spock, being the Federation's envoy, had been speaking directly with Chancellor Gorkon of the Klingon Empire to open treaty proposals. The committee is stunned by the news and debates whether Starfleet will be dissolved.
Science and exploration will continue, however, military efforts will see a significant reduction. Admiral Cartwright protests, saying that the opportunity exists to "bring them to their knees." Spock counters, saying that a peaceful solution is more prudent. In the midst of the debate, it is announced that Kirk will be sent in the Enterprise to the outskirts of Klingon space to escort Chancellor Gorkon's cruiser to Earth for negotiations. Kirk is wholly reluctant, despite Spock's endorsement of him, saying an experienced ambassador should be sent.
However, the council leadership ignores him and closes the meeting. After everyone has left the meeting, Kirk confronts Spock, demanding to know why Spock chose him to escort the Chancellor. Kirk has a high distrust of Klingons, who were responsible for the murder of his son, David Marcus. Spock believes that Kirk, though an unlikely candidate for the mission, should still go, saying "Only Nixon could go to China." Kirk also mentions that the Enterprise's crew was due to stand down (retire) in a few months.
Kirk gathers his crew and the Enterprise leaves Earth. New to the Enterprise is Lt. Valeris, a Vulcan female officer, who is the first of her race to graduate at the top of her class and has been mentored and sponsored by Spock himself.
As the ship races towards the rendezvous point with Gorkon, she and Spock share a ceremonial drink in his quarters and discuss the turning point of Federation relations with the Klingon Empire and their implications. Spock tells her that logic does apply to the events at hand but there must also be some acceptance of faith that the new era will bring peace.
The Enterprise and Gorkon's cruiser, Kronos One, arrive at the meeting point. Kirk hails the Chancellor and invites him and his officers to dinner on the Enterprise that night. Lt. Valeris mentions to Kirk the availablility of an on-board supply of Romulan ale, which she suggests "might make the evening pass more smoothly." Kirk replies, "Officer thinking, Lieutenant."
The Klingons are beamed aboard; the Chancellor has brought his daughter, Azetbur, his chief of staff, General Chang and Kerla. Though both sides are initially pleasant toward each other, and a few toasts to the peace accords and Gorkon himself are made over Romulan Ale, the underlying hostility of both sides still permeates the conversation. The Klingons themselves seem particularly fond of Shakespeare; their philosophical arguments about the peace accords are laced with Shakespearean thought.