When you arrive on Onderron, you are practically seeking out Kavar, your old buddy, and ask him why, exactly, he agreed with the rest of the Council to strip you of your rank, your powers, and your lightsaber, and then exile you to the Outer Rim, even though you came back after Malachor V and faced their judgement. However, first you had to make a pit stop on the moon of Dxun because your ship was damaged trying to run the blockade. General Vaklu started it to prevent evil aliens from the evil Republic from being able to trade evil. He's currently building up a support base for a power grab from his cousin, the beloved Queen Talia. See, Valku figures she isn't strong enough to protect Onderron, so he'll launch a coup and take the throne for himself, thereby leaving that useless heap of a galactic government to fix its own catastrophic problems.
On Dxun, you meet a bunch of Mandalorians led by none other than Mandalore the Preserver. They're there because reasons (Mandalore is kind of a dick). You hop on his shuttle after helping out his soldiers (read: do a bunch of inane quests (see?)) and head on to Onderron to find Mandalore's old buddy who has the contacts you need. You do some stuff on Onderron and eventually attract the attention of Valku, because he's a dick and wants to use your presence and/or minimize the damage you're doing to his support base. You also rescue Mandalore's buddy, who was being held as a suspect in a murder. He sets up a meeting with Kavar in the local cantina. The Master answers some of you're questions, but you're ruefully interrupted by Vaklu's Dragon, the wormy Colonel Tobin. You fight yourself off the planet which is less stable than ever thanks to your actions.
While the civil war rages on, you head off and save another planet (not sure what happens if Onderron's the last one you do). The Mandalorians call Mandalore and tell him and your party to get their asses back to Dxun because the civil war just broke out. You take a couple people to the planet while three other party members attack a bunch of Sith who, of course, are allied with Vaklu. They wipe the floor with more guys than you've ever faced before (best battle ever) while you land on Onderron in a freaking Basalisk War Droid and start killing Vaklu's forces. You make your way to the really long entrance to the royal palace and meet up with some of the Loyalist forces. You fight your way up and find that the door to the antechamber of the throne room is locked, and Tobin is breaking down the force field to the throne room itself with a really big and ugly beast native to Onderron. It's being mind controlled by a Sith, so obviously nothing will go wrong once the shield breaks.
Regardless, you have to get the door open to save Talia. You go through both wings of the palace and murder all the bad guys. On one end, you come across Kavar, who tells you the stuff you would expect to hear from a Jedi Master in the middle of a siege. On the other, you come across an expert slicer, who has kept the door locked and generally made your tour as miserable as possible, what with the exploding consoles, poison gas, and all. You spare his miserable hide and get the door open. Oh, what's this, Vaklu's forces knock the force field down right when you open the door! And wow! The Sith lost control of the beast right after that happened! It kills some guys and packs a crazy-strong punch, but you kill it and head on into the throne room. Talia and Vaklu are fighting with vibros in front of the fancy chair itself, while their forces battle on about them. It's probably the second biggest battle in the game, but I used battle meditation and Talia's forces easily overpowered most of Vaklu's. Kavar shows up and one-shots a couple guys, you duel Vaklu, and then Talia executes the ambitious bastard for treason. She goes off to do stuff and Kavar finally has that talk you've been wanting. He tells you stuff that you probably already know if you've already encountered Vrook or Zez-kai-ell and he teaches you another fancy trick. Talia then rewards you and you leave, never to come back because it's still a stinking hellhole with one settlement worth mentioning on the entire damn planet.