I think the hardest mission is the final Borg mission, forgot the name, but you have NO warp, very little resupply, and stop species 8472 from going through the rifts. Heres what I did I set all of my goals on one thing: Fusion Cube, then I sent it to the middle of the map, as soon as I found out where rift B was I went there and decimated the 8472 fleet! Same with Rift C, then make temporal anomaly station, get your fusion cube close to the top-middle part of the map, activate temporal distortion, send fusion cube in, watch ending

well the hardest mission to me is werewolf, the first Borg mission, because I can't get past it right now. I have only tried it twice as of now, but it seems the hardest so far, because you have no meterials.

NONE OF THEM, they are easy and if worst comes to worst, change the odf files a little heh

Endure the first few minutes of attack.

Use the assimilator's auto-assmililation beam to drain their crew off of their ships and then capture them. If its a good ship like a Soverign or a Negh'Var then you should probably keep it to defend your base.

Eventually, either the Klingons or the Federation will build a metal income station. ASSILIMATE THIS!! Once you do your metal will sky-rocket, then use the Recycler to transmute the metal into dilithium.

Rinse and Repeat and.....Presto!

Hope this helps!