TMP - Have its timeline match up with the real, as it have the film set 10 years after the last episode of TOS, so the ship would've had the last year or two of its five-year mission, undergone a refit and carried out another five-year mission and was partway though another, throughout this time a whole new crew is essentially running the ship. When V'Ger approaches, the new crew of the Enterprise go out to deal with it. Now this could go in one of two ways from here: first being they are the heroes and complete the mission; second is that they are badly hit and take losses, resulting in Kirk and Co having to quickly assemble once again to intercept the invader.