My final post: Scene 3.

This scene starts off with Red X. Still angry with the bad guy he decides to do a one man attack. He heads back to the ship and finds the bad guy. He talks to him and explains his true destiny. He is in fact a living being, but he's genetically engineered. He's been created by fusing the best genetic traits from various beings. He was to be the first of a race of super soldiers under the bad guy's control. As he tells him this the baddy reveals a curtain behind which there are a lot of creatures like him, only these are the prototypes. These are the "Blue X". He sends them after "Red X". Red X tries to flee because he is simply outnumbered (20 to 1 or so). In the middle of the escape this chapter ends.

The next couple of chapters start out in the rebel base. The rebels explain the plan and some arguements are fought out. The flier proves to the critter that the henchman is in fact a good guy now. The soldier gives technical information about the enemy, the henchman knows the base like the back of his hand. The warrior knows the enemy's attack patterns and the rebel boss proves to be an explosives expert. To make a long story short, they all are important.
Now the story line splits again. The plan is for each person to reach a different part of the base and place explosives on strategic parts of the hull. This should take care of the enemies once and for all.
Each character goes to such a point, defeats a boss there and tharr she blows.
You see a cinematic of the Red X escaping and a fex of the Blue X manage to get out too. The base is blown up. An indestructible pod emerges from the ashes containing the big bad guy. He orders the blue X to merge with the Red X and a huge final boss emerges. The player can choose with which hero to fight the boss (except for Red X himself of course) and put and end to the story. The boss is defeated, causing it to unbind and a group of Blue X and of course the Red X fall down. The warrior takes care of the red X. The soldier army finally comes and captures the indestructible pod. The baddy is finally contained. An ending cinematic of pictures and some credits shows how all heroes back home (or wherever) and how they are very happy now.

So, that would be the main part of the story.