Click here to see the hidden message (It might contain spoilers)
What I mean is, Revan is in an Imperial prison at the start of the game, and the Republic flashpoint results in his being freed from Imperial captivity. Then he starts to build an army of battle droids to genocide the Sith Empire, and the Emperor sends the Imperial characters to stop him in the Imperial flashpoint. Even if you try to side with Revan to stop the Emperor (as you can be a light side Sith), he refuses to and attacks you.
Killing the Emperor is only the finale to the Jedi Knight class storyline.
As a class quest, a Jedi Knight could recruit a Jedi Consular, a Smuggler, and a Trooper to fill out his party and all four of them defeat the Emperor, but otherwise those three classes won't face the Emperor -- although a few months ago I had heard rumors that the Jedi Consular also faces him in a different body after the JK kills him, I haven't heard anything to corroborate that since launch. The other characters wouldn't factor into the story, either, e.g. they wouldn't have dialogue options and they'd just be there as support.
Each character class is essentially its own game, albeit with overlapping territory and side quests. If you play as Republic, you'll never set foot on Korriban or Hutta, and likewise with Empire, you'll never set foot on Tython or Ord Mantell. I also believe that you can't visit Coruscant as an Imperial or Dromund Kaas as a Republic player, and I can test that but the servers are offline for a patch currently.
I'm fairly certain as well that certain planets aren't part of the class storylines, so if you stick to the storyline and don't explore at all, you'll never visit certain planets as one class.
I find it curious how powerful these ancient Sith are in the KOTOR era, such as Sion, Nihilus, and the Emperor, considering that it seems like whenever someone from this era (or earlier) somehow survives to the film saga era, they're not even given the dignity of being dispatched by someone of significance, but are ignobly dispatched by some scrub. For instance, Exar Kun by a bunch of barely trained Jedi and Arden Lyn by Laddinare Torbin (who?).