Following the attack on Khitomer, Captain Kirk and his landing party were then taken to Qo'noS as prisoners. On the way there, Kirk was brutally interrogated by Commander Kor regarding Khan and Kirk's mission to Qo'noS. After beaming down to the Great Hall, Kirk and his landing party were then taken to a prison cell. However, Kirk and his party were then freed by two of his officers, Lieutenants Zahra and Kai.
Meanwhile at Deep Space K-11, Commander Spock informed Admiral Richard Barnett and Starfleet Command of the weapons signature present at Khitomer. Spock volunteered to lead a diplomatic mission to Qo'noS in hopes of releasing Kirk and his party. However, Barnett ordered the Enterprise to remain as DS K-11. However, Spock had the Enterprise monitor the Klingon border closest to them. After careful consideration Spock decided to disobey orders and set a course for Qo'noS.(TOS - The Khitomer Conflict comics: "Part 2", "Part 3")
At the same time however, the Romulans and Section 31 commenced their bombardment of Qo'noS. The Romulans were able to destroy the Klingon ship protecting Qo'noS. A Section 31 assault team was beamed into the Great Hall and fought the Klingons. Kirk and his party tried to escape from the firefight but was stopped by Commander Kor, who tried to kill Kirk but was killed by Section 31 agent.
Section 31 then beamed Kirk and his officers to the IRW Raptor One, as Commander L'Nar's prisoners. A Section 31 agent, made sure the L'Nar did no harm to Kirk and his people as they "permanently" destroy Qo'noS.However the Klingons brought in eight of their new D7-class battle cruisers to confront the Romulans. The Enterprise then arrived. Spock was then able to beam Capt. Kirk and his party back to the Enterprise.
However, Capt. Kirk, Lts. Sulu, Kai and Zahra beamed back down to the Great Hall to stop Section 31 from destroying Qo'noS. Kirk and his party were then able to subdue the Section 31 agents in the Great Hall. Unfortunately, they were held at gunpoint by one Kirk's engineers, Lt. Yuki Sulu who revealed herself to be a Section 31 agent.(TOS - The Khitomer Conflict comics: "Part 2", "Part 3")
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