Maybe you were captured because you were betrayed by the one you hold the closest.

maybe you ran into some alien species that was after you while searching in space for an ancient artifact of some sort

So you're liberating planets...From who? A tyrant, a ruthless dictator! But who would that be, it'll ave to be a Zorg player.... I know! Let's use MrSinister... He's the Antagonist you fight against, he kills people who are against him, maims them , destroys their planets....His subjects are afraid of him , but years of brutal oppression have numbed them into passive behavior. It is these people you try to free... But there's a twist in this story....When you were young, you and this very very veeeerrryyyy handsome MrSinister were involved while attending the Space Fleet Academy. You were both very young and foolish then and thought your love could overcome every obstacle..
But due to circumstances (like MrSinister turning into a very violent,ruthless conqueror ), you left him. Now you're on different sides of the fence, although you two still love each other.....
Just my humble opinion on how to make this a epic story

During an Expedition to find the Fabled Planet Zorg... The Empress of Light and her Armada were pulled into a
Black Hole. Instead of being destroyed..she finds herself in a completely different Universe..
Seeking refuge to make repairs and gather food and resources... she finds Planet after Planet.. once filled with Life and signs of Great Metropolis's all dead now... shattered Moons in their Orbits...
Landing Parties return with evidence of a Horrible Weapon wielded by a Heartless Species..as yet unnamed...
whose apparent sole purpose for existence is to feed on other Species... but.... also... evidence suggest another species..also seeming to be from a Universe outside this one.. hunted by the Evil Ones.. who seem to have the Technology to not only travel from one universe to another... but also able to return to them as they see fit...
Hope.... the one thing our Empress was afraid was lost... now is reborn.
She must find these people... and pray they can help return her to her Home... no matter what. (just a thought)

im not good at giving ideas but maybe you could interpret the different universes in this game like massacre xtreme speed and standard into your story and give them different names and different people you run in to.

That would be an interesting story indeed. Is anyone really fantastic at putting videos together? They're not my forte because all I have is Windows Movie Maker...if anyone has skills in that area, I can give you clips and pictures. I just need someone who has better software and more talent. PM me or respond here.

Edit: Here's some cover art I put together. Since this will most likely inspire me to write other stories, I titled it Stories of the Guardian (as others will be "Stories of _________" through the perspective they're told).

This is going to be an awesome self fulfilling rip off story.. all the good parts of all the good legacy bottled down in to one big pile of mashup!!