Star Trek: Encounters is broken up into the five series' and has you go through them in chronological order (or at least as chronological as
Star Trek can be). You start off with
Enterprise, then
The Original Series, then
TNG,
DS9 and
Voyager. Each series has three or four campaigns that take you through some of the major conflicts of that show.
Enterprise has you defending Earth against the Xindi, while in other series', you will have to face off against the Romulans, Klingons and Dominion, and of course what
Trek game would be complete without the Borg?
The game forces you to go through each series in order instead of allowing you to start some missions in the Enterprise era and jump ahead to Voyager. I can understand forcing you to complete the missions within an era in order, but I found it a bit annoying that I couldn't skip around between the stories as I pleased, at least at first. In the end, I went along with it because the further you progress in the game, the more powerful technology and weapons you gain, thus working like a form of leveling up across missions.
There are two gameplay modes in Encounters: Skirmish and Episode. Episode is the story mode talked about above. This is where you will relive many of the major events from the Star Trek universe. And, as you encounter new races and fleets, those ships will be unlocked in the Skirmish mode.
Skirmish consists of three types of short battles. Head-to-Head is your standard Deathmatch style game where two ships plow away at each other until the frag-limit is reached or the time runs out. Battlefest is a little more interesting (at least in my opinion). Here, you and your opponent choose a race/empire. Three ships of the chosen style are picked and the two of you go at it. You each start off as the lesser of the three ships (a Xindi fighter or the NX-01, for example) and each time a ship is destroyed, the next larger one is called in. Whoever runs out of ships first loses. You start off only being able to choose between the Federation (with the NX-01, NCC-1701's A and D) and the Xindi, but as you progress, other races will become available and the Battlefest section will become a bit more interesting.
Onslaught acts as a survival mode and allows one or two players (co-op) to be thrown into a never-ending battle where wave after wave of enemies come at you. The longer you live and the quicker you take out enemies, the more points you earn.