here's one:" the enterprise E is found destroyed. you have to find out who destroyed it"

Most likely series of events would be imo:

1. Contact with the Enterprise-E is overdue. Your ship is dispatched to investigate.

2. Enterprise-E is found, the ship being a total loss. Starfleet orders you to find out what happened to it.

3. After piecing the clues together, your ship finds those responsible and a counter-attack is ordered.

4. Starfeelt decides to make a show of force and reveals the existance of the Odyssey class. In light of the loss, it's revealed one of the freshly completed ships has been hastely commissioned as the Enterprise-F. It's dispatched as the lead ship in a strike force to put an end to the threat and the loss of its predecessor is avenged.

I think decommissioned after Data gets promoted to Admiral. It was a top secret mission after all.

And in the attack the ship is destroyed. And the Enterprise G is commissioned.

One of the best and most well known scenes of Star Trek is the destruction of the Enterprise in ST:III. I think that the writers here have an opportunity to recreate a similarly gutrenching scene for the destruction of E. According to apocrypha both the A and E were named something else and renamed after the destruction of their predecessor. The loss instead of retirement of the ship seems to allow for more closure than just retiring the ship and selling it for scrap (something that wouldn't likely happen during a time of war) I'm thinking your ship is sent into battle along side the E followed by a cut scene sequence similar to the one we saw in the remastered Doomsday mission that shows the crew running for escape pods, followed by the slow and agonizing destruction of the ship. The remaining portion of your mission is to vanquish the remaining enemy ships and rescue escape pods both in space and planet side (ground combat operations). This really should take place during a series of new endgame content, or a FE series with joint KDF and Fed operations (think common enemy like the Iconians).

This changing of the guard (mission title idea here) needs to be epic! Lets face it this will probably be the last cannon enterprise that CBS allows outside of Abramstrek.

I would love for the Enterprise F to sacrifice herself rescuing the Enterprise E Starfleet gets to say the F went out in style, and its gains a real Flagship back.

No thanks. The timeline is 30 years past Nemesis. Trek, like everything else in life, has to evolve. It can't just stagnate doing the same things with the same people over and over ad nauseam. There's a reason why each series had different crews, different ships, even different goals. The idea is to build upon the past not idolize it. There's already too much of this game focused on what was rather then what is or what should be, IMO.

Normally they decommission the previous ship prior to the designation of the new Enterprise, with exception of C and D which went down fighting, but still they preserve the legacy of that ship's name. Besides, Data would have blown up the Enterprise E before letting the borg take it.

I can picture that now;

Data's first officer: Data, blow up the damn ship!

Data with emotion chip: no....NOOOOOOOOOOO! *Smashes console*

I rather think that the ship is reserved by CBS incase they decide to make a movie (highly doubt) but why does every starship named Enterprise meet with a fire ball death? Maybe it's like Voyager and it's lost some where trying to make it back. I don't like any of the suggestions by the OP on what happened to the E either, 1 was in a movie and failed, don't see the reason why Terran empire would want our ENT when they have billions of their own SOV and 3 just doesn't seem plausable, Romulans and Klingons? They dispise each other and Klingons are invading Romulan space...

The E-E got stuck in temporal limbo and returns a few years later, just to find itself replaced by E-F.

Awkward moments ensue.