The Red Alert will start when a time travle mission goes awry, and Einstein ends up on the Enterprise. Taking advantage of the mishap that brought him forward in time, Einstein will travel back in time to kill Hitler, changing the universe.
The Enterprise will be transformed into an Allied warship that requires you to have the last tech level unlocked, and to have researched "Nielsen Ratings". Different skins for it will be available via a horrendously overpriced DLC pack.
When the Enterprise goes into battle, the bridge will move lower into hull. Where it once was a stage will now be, and Frank Klepacki will jetpack down and begin playing the original Hell March.