Does the game Run Saber for SNES come to mind (probably not, because it sucked).
Just a few tips...

1. You said that his motivation was to do the right thing. Nobody roots for the good guy anymore because he has either no real purpose or motive other than to be a hero. Now bad guys and Anti-Heroes on the other hand always have some sort of master plan and a very strong cause. They essentially make the story. Think Snake Plisken (From Escape from LA). This was a character unwillingly thrust into a posisition with a grim chance of survivle by his government (of which he hated). He didn''t care about saving poeple, only himself and found himself risking his neck to save them. The final outcome was completely unexpected.

2. As was mentioned before in this thread, Governments in RPG''s are always manipulative and underhanded. Try employing something similar to the houses of Dune. Rivals who fight over spice production or in your case the acquisition of planetary resources .

Hope this helps...

I think the main problem is that you haven''t identified why your first world is dying. Is it an environmental crisis, solar flares etc...

This in turn affects the missions. If the global mission is to return and save the world then individual missions must lead up to that point. Suppose the world is dying from polluted seas. The planet you go to has an algae that will restore the situation. The main mission is then to return the algae to your world and release it in the sea. But the government objects and so the fight is on.

In that way you have a coherent storyline.

This does sound kinda cool, I especially like the nding you posted, you defeated the bad guys but in the end you decided to do what they wanted, but kept the reward for yourself.

If you want the government to be the bad guys I suggest have all of them good, but then have a section or two that get ambitious and want to have a world of their own to rule that isn't messed up. Say the Special Portal Service (SPS) teams up with the World Environment Cleanup Section (WEC) and decide to run this awesome task in order to scout out a new world to rule, so they request to bring military personnel for security. They end up brain washing the troops into believing they are helping they new races by taking out their primitive governments.

The protagonist feels deceived and used when he finds this out and decides to take revenge on these agencies by stopping their plans. And in the end after defeating them he discovers that he likes this new world and decides to become ruler himself. So he ends up just being a regular guy with his own ambitions, rather than the hero we've seen a thousand times, or perhaps he could be both; the people could just give him the crown for saving their world and he can just sit back and enjoy the rewards with no remorse.

Just my suggestions man. Good luck with the game.

I think that in the intervening seven years, Ruiqing will have already moved past this stage of story development.