Thanks very much for taking the time to review my game and for your suggestions. I can see where it was confusing.
I don't know why the game just started for you. There is a start screen:
Since any keypress or mouse click will start the game I'm guessing when you started recording it also started the game. This will not be an issue for most players. I'll see about making a tutorial to make it less confusing.
The HUD shows Particle Beam and Torpedoes and the help screen (F1) shows the controls for both.
After the transport reaches the first waypoint a new waypoint is spawned farther away and you have to keep protecting the transport as it navigates to the next waypoint. I will add a message after Waypoint Reached saying "Next waypoint in 3000au".
You can't "win" the game you just try to survive as long as possible and get as high a score as possible. Your score is based on how many waypoints it reaches successfully as well as how many enemies you destroyed. You even get points for shooting asteroids :