The game needs a story. Something that has been lacking in Star Trek for more then a decade now, not taking into account some star trek online narratives and of course the odd quality fan-fic. But this isn't a straight Star Trek story, it is a parody that takes aim at the current iteration of terribly write nonsense Trek caused by overrated writers and directors like JarJar Abrams and Alex Kurtzman. So the "levels" in the game should address themes on faults in modern Trek as committed by that cabal of gimmicky mediocrity.
The format for the game is pretty simple. Although the current writers would not understand such a structure, the game has a beginnings, middles and an endings. This structure will be used for the overall structure as well as the levels.
A level will have an introduction where a new character can enter and a new foe can appear. Then the middle of the level will be a strategic battle with the current enemy. A level boss will typically end the level, resulting is a completed arc as it should be! The overall narrative also should have some of this structure.
Level 1 : Introduction.
This level will set up the story and contain a training level to get used to the controls. When the backstory is established, some characters are introduces such as Nog and the Gorn, a simulation of the Jem'Hadar ships will train the player in using the phasers. When this is completed, the conclusion to this level will be the Defiant going to pick up Jake Sisko.
Level 2 : Illogical
Arriving at Risa, the Defiant picks up Jake Sisko. As a successful writer, his talents will be welcome on the coming adventure.