or a variation of 'The Ultimate Computer'
1. The Enterprise (or Players ship) was not selected for the M-5 Refit. A Vengeance Class DN (I really Doubt that with Klingon Hostilities on the horizon that Starfleet is going to simply shelve that design) (U.S.S. Confederation) is refitted with the M-5 system.
2. The M-5 actually DOES function as advertised, the programmers being Genre Savvy and seems to be a good system to be used as MFD and ships AI.
3. Given the prevalence of drones these days, the M-5 has the ability to run various unmanned assault fighter wings efficiently.
4. The Klingons find out about the war games and attempt to destroy the ship through means gross and subtle. The M-5 recognizes them as a priority threat and shreds them in short order. The Confederation crew doen't really have much to do as M-5 does most of the leg work, giving it praise.
5. It starts going wrong: perhaps something missed in programming, or perhaps the M-5's programming works far too well, but M-5 has no qualms about heading for the klingon border and commencing raids on Klingon facilities. The Klingons will have severe problems with the ship as it reacts far faster than they do.
6. M-5 does not particularly regard SF vessels as enemies as it's screwed up programming still thinks it's in Wargames simulations. It will disable SF vessels as part of the wargames. It will have no compuction eliminating KDF Vessels
A brave little theory, and actually quite coherent for a system of five or seven dimensions -- if only we lived in one.
Academician Prokhor Zakharov, "Now We Are Alone"