[q]Drink a cup of real tea and step (most improbably) out of your starship onto the surface of an ancient world. [/q]
That sounds like “The Restuarant at the End of the Universe,” but I wasn’t aware that there was a video game.
After rescuing your brother from a crazy transvestite, you escape antarctica
That would be Resident Evil: Code Veronica.
The Soviet Psychic who threatened to take over the world thinks he has the last laugh when he steals the time machine, but it was not charged properly and sends him into the prehistoric era. Then he gets eaten by a Tyrannosaur.
The Ancient’s efforts to wipe out their enemies through solar flares is thwarted when their world is destroyed by a Black Egg.
The Ancient’s efforts to wipe out their enemies through solar flares is thwarted when their world is destroyed by a Black Egg. Much thanks from every other race in the universe. Then you get attacked by the Uthleks and blast your ship back in time, in an endless time-loop.
Starflight?
Red Alert 2: Yuri’s Revenge
Hitchhiker’s guide to the galaxy. They never made Resturant. Damn them for ending the game on a cliff hanger.
Hitchhiker’s guide to the galaxy. They never made Resturant. Damn them for ending the game on a cliff hanger.
Planescape torment?
Ecco the Dolphin
I got some.
PC:
-You save the world, and then walk away from the President.
-You are led away by the cops, having saved the world, but are believed to be the bad guy.
-You step on a train, and ride into the unknown
-You find the bad guy, but are saved by the loved one you set out to save.
-A genocidal madman is killed, in Victory or Defeat.
SNES:
-You escape from a sinking ship, only to be browbeat by your rescuers.
-You return home after beating up the divine.
-You save the world from Nothing.
NES:
-You save an alien race from extinction by playing with cubes/blocks.
Homeworld. Good presentation on the story.
[hijack]
I have to say a few words about System Shock 2.
It’s a great game, and it’s just fine until you defeat The Many, at which point it starts going downhill. The ending sequence is disappointing. The big dumb shooting match is so un-shock-like, and the final cutscene, just bad. I think they just started running out of time, the game from The Body of the Many onward seems very rushed and totally different from the execution of the rest of the game.
Quoth drayton:
Now, if that were Melinda (the Mental Marvel), that’d be “Chip’s Challenge”, but Miranda? I don’t know.
How about these:
You defeat the commander of the city-state’s forces and take his really nice sword, but you can’t really do anything with it because you’ve already killed all the enemies.
You kill your evil half-brother just in time to prevent him from following in your father’s footsteps (or trying to, at least).
Balder’s Gate?
From HPL:
Grim Fandango, one of the greatest adventure games ever.
How about this?
After shooting down a former companion who stole a star, you head back to Manhattan for a night on the town with a comely pirate wench.
HPL got Hitchhiker’s Guide and Ecco… good show! And yeah, damn Adams for ending it on a cliffhanger.
Journeyman picked up on Homeworld… I tried to keep that one sort of vague. Besides, Karan S’jet (the “young neuroscientist” in question) is my favorite character. I even wrote a story about her, my first and only piece of fan fiction.
Nobody’s gotten my last one, though, but it’s a toughie. Not a very popular game, either, though it got almost universally-excellent reviews. A second hint: "Stuck. Won’t budge."
Not that I’m doing much better… I’m stumped on the newest offerings.
Grumble, grumble… I haven’t played the game in four years (darn computer crash), but yes it is Chip’s Challenge and the girl is Melinda.
That sounds like Q-Bert, but I never finished the game nor got the point of it.
Here’s another:
You fall to Earth from space after beating the bad guy and land on the wing of your partner’s plane (Hint: Two games starring the same character fit this description.).
I must now hunt you down and slay you with a laser rapier! 
Here’s some to nibble on:
*You hurl the world into chaos and pain when you choose to not sacrifice yourself.
*It’s time to choose: Either you hypocritically give in and work for those you have strove against this entire time, or you can engage in a battle you have no chance of winning. It’s your choice, after all.
*You escape from the drowning city after tricking your foes into turning themselves into “gods”.
*You crush the enemy commander’s face under your heel, ending the thousand year war and ensuring that humankind will live as flesh and blood instead of wire and silicon.
*The great destroyers annihilate an entire star system before disappearing. You stay behind to save thousands of the fleeing refugees and die in the massive explosion.
Oh yeah, Torment was a great game. Too bad it never got the attention it deserved. 
The first one is Half Life.
Second is Indy and the fate of Atlantis.
Total Annilation?