This almost sounds like the same premise as 'The Orville'. I'd like it a little more of 'Starfleet has said that you've gone over the line one too many times. After barely avoiding an all-out war with a normally neutral race, they've decided that you and your crew are best set to black ops work - those missions that Starfleet has wiped off the books (or don't even know about if you want to use an Admiral in starfleet that is sorta rogue, natch) and your ship is supposedly heading to the scrap yards at Surplus Depot Z13 - your first mission - steal your ship!' That said, I hope you're successful!
That's kinda the missions we will be doing. Spoilers: The Admiral is part of Section 3. His ID is a false one and the crew, depending on how they handle repairing the ship will be inducted into Section 31 to find out who caused the Romulan Star to go supernova so quickly and what the Orions have to do with it. All the while the bigger mystery is why there are so many temporal anomalies and who is killing off former agents of the Obsidian Order, Tal Shiar, and Section 31. Loads of fun brewing.
And thanks for the hope of success! I appreciate it :)