At one point Chang announces that his people need "breathing room", whereupon Kirk mentions that the same thought was expressed by Adolf Hitler in 1938. Azetbur speaks of the Federation being a "homo-sapiens-only" club, despite Spock's presence. Gorkon concludes that there is still much work to do. The Klingons leave and the Enterprise crew (literally) breathes a sigh of relief. Chekov mentions that their visitors had "terrible table manners" and Spock says their own behavior, was fairly unacceptable as well.
Resting in his quarters (and making a log note that Romulan ale is now banned from all diplomatic functions aboard the ship), Kirk receives a call from Spock to report to the bridge. Hung over, Kirk meets with Spock, who tells him a huge, unexplained neutron radiation surge has been detected on a scanner. As Spock and Kirk try to find it's origin, Kronos One is suddenly hit by a torpedo blast which appears to come from the Enterprise. The Klingon cruiser is hit again and begins to tumble helplessly, losing thruster power and their artificial gravity.
On board Kronos One, two figures, wearing Starfleet space suits and magnetic gravity boots, beam aboard and begin to fire upon the Klingon crew with phasers. Several are killed, one is wounded, losing an arm. The assassins move through the ship, finding the Chancellor's chambers. The two Klingons with him are immediately killed, and Gorkon is shot through the chest. The assassins walk back to the transporter pads and beam out, trailing some Klingon blood with them.
Chang hails Kirk and immediately accuses him of the attack on the ship. Kronos One moves into an attack positions and activates its torpedo cannon, preparing to fire on the Enterprise. Kirk, knowing that the attack would be deadly and spark an interstellar war, surrenders immediately. He offers to come aboard Kronos One and McCoy volunteers to go as well for medical assistance. As Kirk leaves the bridge, Spock surreptitiously touches his shoulder, placing a small object on his uniform.
Kirk and McCoy beam to Kronos One and are escorted by Kerla to the Chancellor, who lies bleeding and dying on the deck. Chang tells them about the assassination and accuses them of lying when Kirk claims innocence. McCoy demands to treat Gorkon and does, however, his unfamiliarity with Klingon internal anatomy prevents him from doing more than reviving Gorkon for a few moments.
Gorkon gestures for Kirk to approach him and, putting his hand on the back of Kirk's neck says "Don't let it end this way." He dies. Chang immediately places Kirk and McCoy under arrest for the murder under the Federation's articles of interstellar law.
On board the Enterprise, Uhura reports the arrest. Spock assumes command of the ship and orders a general standing down, knowing they cannot attack Kronos One to rescue Kirk and McCoy. Uhura also receives a message from Starfleet to return to Earth immediately, however, wishing to investigate the attack on Kronos One and Gorkon further, Uhura relays a fake report that the ship is experiencing multiple malfunctions and cannot return until they are repaired.
On Earth, the Federation president meets with several other council members about the incident. Among them is the Klingon ambassador, who defends his government's arrest of Kirk. The Klingon ambassador also cites, as Chang did, Federation interstellar law. Vulcan and Romulan ambassadors Sarek and Nanclus agree, as does the president, who does not want to provoke the already delicate relations with the Klingon Empire. A daring rescue plan, proposed by Colonel West, is dismissed by the president as well.
In Gorkon's place, Azetbur is appointed chancellor and talks directly to the president, saying Kirk and McCoy will stand trial on Q'ono'S. She also affirms her reluctance to attend the peace accords, but agrees, saying that the location must be kept secret and that any attempt to rescue Kirk and McCoy will be an act of war.
The trial begins; the prosecuting attorney is Chang himself, while Kirk and McCoy are defended by Colonel Worf (a cameo by the character from Star Trek: The Next Generation). Chang delivers the charges, that Kronos One was fired upon, the assassins came from the Enterprise and that Kirk ordered the attack. Though Worf successfully dismisses the final charge, Chang is still able to lay the conduct of the two assassins on Kirk, saying, as captain, he is responsible for the conduct of the crew under his command. Kirk does not deny the charge.
When McCoy is questioned about his attempt to revive Gorkon, Chang attacks him verbally, challenging his medical expertise based on McCoy's age. He also cites the fact that McCoy, along with all the other dinner guests, consumed Romulan Ale that may have affected his ability to aid the Chancellor. The most damning evidence that influences the trial is Kirk's own words, possibly stolen from his personal log, where he stated "I've never trusted Klingons, and I never will. I can't forgive them for the death of my boy."