Game Manual
The game manual that comes with the game houses more information of what is possible in the game than the game actually tells you during normal game play. Due to this, it is best to read the manual thoroughly before you begin playing. For example, you don't find out that any military bases you build will be able to automatically repair friendly ships that are nearby unless you read the manual. This knowledge comes in handy when fighting with the enemy ships and one of the friendly ships is taken down.
Military Bases
While military bases are helpful, it is not necessary to build a lot of them. The best way to make use of the military in the game is to station many guards around all active jumpnodes, so they attack any unwanted guests that come through. You can also build corvettes and cruisers and station them around the vicinity of the jumpnodes, because eventually your military fighters will get replaced by the machines as you progress in the game.
Mines
Throughout the game, there are mines you need to destroy. You can find two of them on the left asteroid field toward the center-right. Take the bigger guns for protection during this mission as the mines are heavily guarded. When partaking this mission, stay away from the crippled space station. You would be brought into an unnecessary battle that is very hard to beat. It is best to stay away from it.
Making Your Choice
During one point in the game, you must make a choice of which side you're on. To make your choice known, you must send a force-fire by pressing "CTRL" and right-clicking on the empire you decided to fight against. Once you do this, the other side will send you a welcome message thanking you for the help. The group you sent the force-fire to will automatically think of you as the enemy.