Events go fast now. You get arrested. After that you can flee with a ship. Just fly wildly around with full speed and don't let yourself be shot down. Then you jump to the Don's base and dock with it. Next you jump back into Duke's Domain.

A ship is coming at you, so just shoot at it with your ion disruptor until the pilot jumps out. You get transported into it and it's your turn to attack the Nividium station. There are four spheres that create power for the station's cloaking device. When you get close enough you will see them. Destroy them and the cloak will fail.

The Paranids escape to Heretics End. Your job is to fly to a station surrounded with enemies. Get very close to the station, to that sqare you will see when you are close, and the gate will be created. Done with that, Khaak attack. Take them all out. Take care of all the small ships, scouts and fighters. Once they are all gone attack the big ones, but shoot at them from a distance (when you hear you are within range). If they start to fire at you, fly away, then approach again. Another wave appears and there is more fighting going on. Again, concentrate on the small ships. When you reach a certain point you will see a lot of plot happening in a sequence and a huge fight going on.

Next time you can do something, you find yourself in some sort of tunnel. Shoot at the round generators (you know how they look from the Pleasure Complex) and evade the debris flying towards you (left side around is a good way to avoid it). When the station explodes, lean back and enjoy the fireworks.

Congratulations you've completed the X3: Reunion Story.