This guide teaches you how to use a ship to beat any mission in the game.
Find your ship and get a mission
This step is very simple. Go into your pod and fly around until you find a ship. Any ship that has at least one gun will do. Secure the ship and fly it close to a station. Do not fly it into the station because that will sell it. Go into the station with your pod and get a mission. Then, fly back out and control the ship again. You can do this in the opposite order, but I do it this way for missions with time limits.
Snipe the Other Ship
Now, match the other ship's speed. The orientation of your ship matters on the type of mission. Hold down Q, and pan the camera so that you can see the other ship. If you have matched the speed, the ship should appear to be still. This is where the steps diverge for different missions.
For assassination missions, orient your ship, so there are no rooms between your ship and the target room. Right click on the room, and the missile will lock on and blow up the target.
For capture missions, blow up the room next to the person. Then, get out your pod, and pick up the target.
For rescue missions, you can usually do the same thing as capture missions, but there are often walls surrounding the target on three sides, so you just shoot at all the rooms around the target, which detaches it from the ship. Then, you can go into the room with your pod and get the target.
For steal missions, blow up the room next to the box, and use your pod to get in and steal the thing.
For hijack missions, blow up all rooms except the pilot, the engines, and a line of rooms connecting the first two. Then, there are less enemies, and you can easily finish off the ones left.
This even works on glory missions with toughened hull. There is a bug where you can blow up the engines even though you shouldn't be able to. There is also a bug where you can blow up any room that is next to a blown up room. Using this, you can destroy the ship from the engines up. If you are quick, you can even blow up the telepad before the target has time to escape.
Now you know how to beat any mission in the game using a ship. Hopefully you can put this to good use and get some really high glory scores.