The following is what I am proposing as canon changes to the game. After each entry where needed I have included comments and what the changes are.
I will follow this up with some questions that I am interested in seeing the answers to.
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Everything from TOS (series), TAS (some eps) and TMP, TWOK and TSFS are canon (even the inconsitencies )
2286 - When an alien probe on the search for the extinct humpback whales threatens Earth, Kirk and his crew travel to the past in a Klingon Bird-of-Prey. They find two whales in the Cetacean Institute in Sausalito and manage to take the whales with them back to the 23rd Century. For his effort, Kirk is reduced in rank from Admiral and assigned to command the new USS Enterprise (formerly the USS Yorktown NCC-1717). In protest the Klingons remove all ambassadorial staff from Federation space. ("Star Trek: The Voyage Home" - Modified)
Only a minor change. That being the Yorktown keeps her NCC. IMHO the name Enterprise is far mroe important than the NCC 1701. I never liked the whole A, B, C, D, E etc thing. So I am taking this chance to remove it. So the new Enterprise is NCC 1717, otherwise the movie remains as shown.
2287 - Spock's illogical brother Sybok seizes control of the Enterprise and with his telepathic abilities he influences the crew except for Kirk, Spock and McCoy to head for the edge of the galaxy where he believes is the planet Sha-Ka-Ree. At their arrival the landing party is received by a strange being that claims to be God. The incident is classified by Starfleet at the highest levels, Sha-Ka-Ree is quarantined as per General Order 7. ("Star Trek: The Final Frontier" - Modified)
Okay here comes the start of the major changes. Sha-Ka-Ree is not in the center of the Galaxy bout out near the Galactic Barrier. And God, is Gary Mitchell. He has regenerated and used Sybok to lure Kirk to him for revenge. We can keep the Klingon BOP that hunts him, I don't see why not. In the end, Dr. Dehner (Sally Kellerman = yummy) also appears to Spock, as Kirk is fighting Mitchell for his life on the planet below. She convinces Spock to use the Nav Deflector to create a Genesis Wave that will release Mitchell from his tormented existence. In the end it does, but also transforms Sha-Ka-Ree into a lush paradise. Mitchell and Dehner are now like true Gods or Cosmic beings and they promise to raise a new race of humans on Sha-Ka-Ree that will someday bring peace to the Galaxy. Kirk agrees to quarentine the planet and they are sent home.
2291 - The Klingons learn of the Sha-Ka-Ree incident and declare that Captain Kirk has, on behalf of the Federation, has continued to develop the Genesis weapon. Sighting that this spells nothing less than the doom of the Klingon Empire, a Klingon attack is launched against multiple Federation and Starfleet locales along the border. War is declared by both sides.
Now here is another point I should make. I don't like TNG Klingons (no offense to everyone who does) I prefer the John M Ford style (minus the FASA Fusions) and therefore use them. But in the back is the Cult of Khaless who wish to return the Klingon Empire to one of honor. So there is a bit of it, just not the over the top Samurai-Biker-Vikings TNG gave us. Also "How did the Klingons find out?" I figure Klaww was at Sha-Ka-Ree, but Gary Mitchell (or Dehner) put a memory block on he and his crew, but perhaps he remembered years later (strange nightmares?) and that lead to the discovery. Regardless of how, we know have our Klingon/UFP that so many of us wanted to see on screen.
2292 - After the disastrous explosion of their moon Praxis destroys billions of lives on the Klingon Homeworld, the only surviving High Council member Chancellor Gorkon offers peace to the Federation. A joined conspiracy of Klingon and Starfleet officers, however, strives to obstruct the peace plans by all means. Gorkon is killed, and Kirk and McCoy are arrested and condemned by the Klingons. After they have been freed, they head for the Khitomer peace conference, where they defeat the traitors with the help of the U.S.S. Excelsior and Capt. Sulu ("Star Trek: The Undiscovered Country" - Modified).
Yes I know the fans love this movie. Yes I know it is a fav of many. But it still had problems and I can't forgive them, so instead I will change them. Quickly. Valeris is not Valeris but Saavik. The Excelsior draws the Klingon border patrols off, while the Enterprise slips across the border. There are others, but in the end the movie still ends the same way so all is well. On a side note I moved Praxis to the Klingonhomeworld (which I use as Klinzhai) so that it made more sense for the entire empire to be thrown into chaos. O'onoS is the homeworld of Gorkon and therefore the site of the new homeworld.
Captain Kirk finally retires from Starfleet and is hired by the Chal government to head their defense fleet. While the incident is classified, what is know is that the decommissioned USS Enterprise (Donated by Starfleet to the Chal government) is destroyed as well as the traitorous Command Starfleet Admiral Androvar Drake ("Star Trek: Ashes of Eden").
I loved this graphic novel. I haven't read the actual printed novel, but I recommend the graphic novel, except for that drenn about Klingon shields tuned only to repel phasers, that was just stupid.
Shamed by this second case of corruption within Starfleet in the same year, the Federation president reactivates James Kirk at the rank of Admiral and orders him to become the new Commander Starfleet. Kirk agrees, but requests a short vacation first to prepare himself.
Captain Spock retires his commission and joins the Federation
Diplomatic Corps.
While on route to Earth to assume his position as Commander Starfleet, Admiral Kirk's shuttle fails to check in at Epsilon XII. A massive search of nearly 60 ships fails to turn up a trace. Admiral Kirk is reluctantly listed as Missing.
He always said he would die alone
2293 - Retiring from Starfleet, Scotty embarks the U.S.S. Jenolan to continue the search for Admiral Kirk.
I liked this aspect from the TNG ep, too bad Generations made it invalid.
Admiral Robert Wesley is chosen over Admiral Hunter Styles as the new Commander Starfleet. Wesley's address to the Fleet (Broadcast on the Federation News Net) praises the ideals of Admiral Kirk and proclaims that "from this day forward there will always be a USS Enterprise and she will always be the Flagship of the Federation."
So there it is. Comments are welcome, but this is set in stone. A more developed timeline will come with more information to fill in the blanks, etc...