The NX starship is a prototype ship, that means when you scan enemies, you can then also jam certain functions, like their shields, comms or weapons. You are sent out on a mission to find a home for the Vulcans, and for some reaon the Klingons have developed a Protomater weapon, which you stumble upon. The final mission is you, and a small fleet go and intercept the Klingons, break the shields down, beaming the weapon off and voila, done. There are only 5 missions in total, and involve things like warping to different system, scan stuff, blow up some ships, scan more stuff, disable shields to beam stuff up (whilst your shields need to be dropped, meaning you take damage).