Taking the books, and comics into effect the Federation had access to many friendly Klingons before 2293; Konom who served on the Enterprise, Bernie the half Human/Klingon; Dr G'dath an exiled scientist who helped Kirk in 2271; Maltz who was captured over Genesis; plus undoubtedly a ton more- so wasn't it odd Dr McCoy didn't know enough Klingon anatomy to save Chancellor Gorkon?
So What If... Dr McCoy had saved the Chancellor?
Dr. McCoy manages to save Chancellor Gorkon- his time with Konom, and general reading up on Klingon anatomy had rewarded him well. The patient was resting while Kirk was explaining to Azetbur that he would open his ship up to Klingon inspection to prove the Enterprise did not fire on Kronos One - while skeptical of the Human's claims she agreed and sent an engineer and a security expert over the Federation ship.
Spock had already started an investigation- he was convinced there would be a logical reason for what the view-screen showed and what Scotty was insisting didn't happen. He had assigned Chekhov to act as liaison to the Klingon's on board, and Scotty had promised co-operation. Spock has also initiated a full communication jam, ordered full sensor sweeps, plus extended the Enterprise's shields over the Kronos One. He starts going over the logs of the attack convinced the reason is there.
Kirk does not leave the Chancellor's side, and they talk when possible. Kirk reminiscing about his adventures, and touching on his anger towards those that had killed David. He wanted to hate 'all Klingons' he tells Gorkon, but after meeting Konom, and even Maltz he realised not all Klingons are the same. Gorkon in turns shares the stories of how Kirk is a bogeyman to some Klingons, and how his actions had removed more than one Chancellor or House from power, even if the Federation knew nothing about it.
Day Three: Repairs are nearly finished on Kronos One, while the Enterprise crew have found the boots, but no assassins. The visual inspection of the armoury has indeed proved the Enterprise did not fire, with both the visiting Klingons in reluctant agreement. Spock and Azetbur meet and agree to send a joint statement to both Governments. It will state there was an attack, but the Chancellor was fine, and the conference must be moved from Earth. The transmission is sent, and was suspected both versions had encoded entities tacked on. Spock starts work do decode the additions, and Azetbur sends a Klingon brigadier called Kerla to help him. Meanwhile Kirk has made an ally of Gorkon who Kirk has realised is sincere about creating peace between the Empire and the Federation. Gorkon invites Kirk to Qo'noS, and Kirk offers the Chancellor a tour of Earth.
Spock, and Scotty have come to the conclusion that the build-up of neutron radiation which happened just before the torpedoes fired is evidence of a cloaked ship firing from below the Enterprise. Spock wants to go on-board Kronos One to confirm his findings which Kerla agrees to arrange. Instead of beaming to the Transporter Room however, Kerla and Spock beam to a cargo hold, where Spock is attacked by the Klingon. Spock however proves that Vulcans are quite adapt at physical combat, and holds off his attacker until help arrives in the form of General Chang who disintegrates Kerla. Taken to the Klingon's sickbay, Spock's ruffled appearance startles McCoy and Kirk, but the two plus Gorkon, and Azetbur listen as the Vulcan relates his theory about the attack on Kronos One. Chang finds the idea of a BoP that can fire through cloak laughable, but Gorkon grants Spock permission to access Kronos One's logs.
Scotty is finding all sorts malfunctions appearing all across Enterprise's system. Computer glitches, pipe failures, tampered equipment. He reports it to Spock and Kirk, but is otherwise firefighting the damage.
Day Four: The two ships get their answer as USSExcelsior warps in and the IKS Dakronh, decloaks. On-board Excelsior is Admiral Cartwright, who has come to escort Chancellor Gorkon to the rearranged meeting point on Khitomer. With Kronos One ready to warp Kirk returns to his ship, while McCoy stays with his patient. Spock having got the data he requires tells a meeting of the assembled Federation brass that Enterprise was the innocent party, and a cloaked ship fired on Kronos One. He provides data that shows the trajectory for the torpedoes was wrong to be from Enterprise and also reading from the impact sites that show the damage was not caused by Federation weapons. Admiral Cartwright promises a full investigation.
The small fleet readies a jump to warp, only for the Enterprise's engines to fail just as the other ships jump. Scotty is left with only one opinion: sabotage.
Captain Sulu is enjoying a tea in his quarters on-board Excelsior when he assaulted and ko'ed. Several other senior officers are also incapacitated. Admiral Cartwright assumes control of Excelsior.
Scotty and Spock manage to find a virus written into the Enterprise's computer code. Scotty does a cold restart of the engines while Spock recognising the code scripting, confronts the author of the code: Lt Valeris. The Vulcan refuses to answer any questions forcing Spock to mind meld with her and rip the info he needs from her mind. He tells Kirk that the Dakronh is the ship they are searching for, plus Chang and Cartwright mean to kill the Federation President. Scotty nearly kills himself, but he gets the engines online and Enterprisewarps to Khitomer.
Day Five: Serving on the Enterprise dished up all sorts of surprises, so Sulu is totally unsurprised to find himself locked in his cabin, and his ship usurped. Also, having served on Enterprise Sulu has prepared for such an emergency and picks the lock on his door, stunning the guard with the spare phaser he kept hidden. Free, Sulu finds his other senior staff also prisoners and sets to work freeing them. As they do Excelsior arrives at Khitomer, wherein several Klingon Warbirds decloak and start firing on Excelsior, which fires back- though her fire seems targeted at Kronos One. On-board the Kronos One Chang shows his colours by transporting out, dropping the shields as he does. Kronos One starts taking serious damage, leaving McCoy fighting to keep Gorkon alive.
Sulu and his officers split up to try and sabotage the Excelsior's ability to fight, and one team led by Janice Rand manage to disable the torpedo launchers, while Sulu's team storms the bridge wearing MACRO armour – they fight through the soldiers on the bridge to regain control. Sulu managing to stun Cartwright out-write. As he is fighting Enterprise drops out of warp (having strained her engines to almost breaking point) and immediately positions herself between Kronos One and Dakronh which cloaks. Kirk orders Spock to find it while directing fire at the remaining hostiles. Enterprise takes a ton of damage from Chang's ship- including a full hull breach. Sulu's crew gets the phasers on line and helps finish off the Klingons while being pummeled by the Dakronh. During the battle Spock realizes that Dakronh is still going to vent ionized gas as an exhaust. Uhura suggests using the equipment they have on-board to catalogue gaseous anomalies as a guidance system- Spock starts making adjustments to a torpedo.
On Kronos One McCoy finds himself in sickbay, fighting alongside Gorkon as Chang's people try to kill the Chancellor. McCoy takes a shot for the Klingon, just before Azetbur leads a force in that saves them. Chang goes for a killing blow on Enterprise just as Spock has his torpedo ready. Chang's photon torpedoes smash squarely into Enterprise's engineering hull, crippling her and causing a warp core dump- Chang's triumph is short lived as Enterprise's modified torpedo hits the Dakronh - Sulu spots the explosion and trains his weapon on it causing the Bird-of-Prey to explode.
Kirk barely has time to explain the assassination plot to Sulu and Gorkon as he is running to the transporter room. After a quick search, Kirk finds the Federation President Ra-ghoratreii in the main auditorium with the Romulan Ambassador Nanclus, who was also implicated in the Conspiracy. As Kirk ran towards them a shot rang out and Kirk dived on the President, getting wounded in the shoulder for his trouble. Azetbur, who has beamed in but a moment earlier with Gorkon and McCoy, draws a phaser on the Ambassador. Scotty meanwhile shoots the would-be assassin through his own sniper window- someone McCoy will identify as Colonel Duras of Chang's staff.
After the smoke clears, and the delegations for Chancellor Gorkon and President Ra-ghoratreii begin the process that will lead to the Khitomer Accords, it becomes clear Enterprise-A is no more- her engines are fired, her hull compromised, and her systems crippled. Starfleet was about to de-commission her anyway and scatter her crew, but as Gorkon reflects this way she went out fighting, as a Warrior should. The senior crew gather on her shattered bridge to reflect before they are sent their separate ways. Scotty will see Enterprise's remains home before transferring to Starfleet ship design; Uhura will began teaching at Starfleet Academy; Chekov was transferring to Excelsior as First Officer under Sulu to replace the officer lost fighting Chang; Spock would be taking command of a diplomatic vessel; Captain Kirk however had no plans- he was unlikely to get another command at his age, but did not want to be bumped to the Admiralty, he'd tried that, and it wasn't to his taste.
Summoned to a meeting with the President and Chancellor, Kirk is floored when President Ra-ghoratreii offers him the chance to become Federation Ambassador to the Klingon Empire- Gorkon tells him that his actions will have brought him much honour in the Empire, exonerating him of his past deeds. Kirk is surprised, and delighted to accept. Gorkon is very pleased they will be "exploring the undiscovered country of the future together".