Starfleet Command II: Empires at War is based on the rules for Starfleet Battles, a board game published by Amarillo Design Bureau. Getting this game to work under wine is pretty straight forward, but following this HOWTO may help you avoid some common pitfalls.
The game comes on 2 CD-ROMs, so you need to make sure that your wine environment has properly set up your CD-ROM drive. For complete information, refer to the Wine User Guide.
To start the installation, insert CD 1 into your CD-ROM, make sure it's mounted (mine is mounted in /media/cdrom), then run 'wine /media/cdrom/Setup.exe'. When prompted to change the CD, you will need to have a terminal window open and use 'wine eject'. After inserting the second CD, make sure it's mounted and then continue the installation.
Updating to latest version
Since the original retail release, there have been several bug fixes and other enhancements, including new missions, published by Taldren. Taldren closed their doors, but the SFC2:EAW community still has activity, and Dynaverse.NET has taken over hosting updates, and providing support for the game. Dynaverse's main website includes links to download the latest patches, add-ons, and a few other utilities. There is also a user forum that can provide some help in tactics, and general chat about the game if you're interested.
After a clean install, visit Dynaverse's SFC2:EAW Download Page to get the most recent patch.
Since you just did a fresh install with no patches, you'll want the 2002-2036 Patch. Download this and save it in the same directory you installed the game. When the download completes, you can run 'wine SFC2Patch2002-2036.exe' to patch the game to the latest version.
You can also download any of the other utilities if you want, but I haven't tested them yet.
You can optionally download the directory server updater if you want to try to get on the Dynaverse and play multiplayer.
As of 1/5/08, no SFC2:EAW servers appear to be up and running (there are a couple for SFC2:OP, but they're not compatible), so you most likely will have the game hang while trying to connect, unless a server comes up. You can check the servers' status on the Dynaverse main page.
Before starting the game, I suggest using the setup utility to set the game's resolution. From your installation directory, running 'wine SFC2Setup.exe' will let you pick from the available resolutions. In older versions of wine, hardware resolution caused strange red "ghosting" of all images in game, but as of 0.9.52, hardware rendering works just fine with an nVidia video card (I haven't tried it with others). If you experience strange ghosting or slow graphical updates, make sure you have the latest drivers for your video card, and try disabling hardware rendering if you really have to.
You can set your wine environment so that the game either runs in a windowed, "virtual desktop" or full-screen. For more information, see the Wine User Guide.
The first time you start the game, you'll be prompted for your CD-Key. This should be located on the jewel case on a sticker. If you've lost it, you can contact the moderators at the Dynaverse forums, and they can issue you a new key (at least, that's what I've been told).
To start the game and view all the intro movies and so on, just run 'wine SFC2.exe'. If you want to skip the movies (you should watch them at least once, though!), you can just run 'wine StarFleet2.exe'.
That's it! You should have your game running, and can select the Single-Player Campaign from the menu and go for the tutorials.