Okay... Here are my suggestions.
(PLOT OUTLINE) The planet we start on should be Nar Shaddaa. Scum, villainy, and several characters should be there. They meet up, and one of the characters is being tracked by stormtroopers. A classic Docking Bay 97 event occurs, and the current charries escape. They reach Farfinn for a smuggling run, and there they meet up with my Twi'lek bounty hunter(and maybe someone else), who teams up with them while simultaneously killing her former employer as a bounty. They escape, but Risa is captured by Stormtroopers on the planet(and the Dark Jedi). The crew follows, coming to a nice, big, menacing space station. They go on and rescue Risa, and escape, heading to Coruscant. They land, transfer cargo, and escape when the Empire finds them (with the help of a local crime lord and his forces)
The crew then proceeds to Mygeeto, where their warehouse is located. They spend a little time there, and the charries get to know each other better there. They eventually leave, and they go on a run to Tatooine. Here, before they can get their cargo paid for, Jabba gets pissed at a crew member and runs them off. So they leave and go to Rodia instead. But the ship is shot down by one of Ara's former bounties and his pirates, and they crash in the jungle. Luckily, they repair their ship with the help of a band of Rodian outcasts, kill the pirate group in question, and leave. Eventually, they reach Dantooine. Landon the Jedi Hunter then reveals his true colors. The Dark Jedi and his bodyguards arrive there, and the entire crew is captured and brought to the Star Destroyer. One of the crew evades capture though, and sets the rest free. They fight their way through the stormtroopers to the bridge, where everyone fights against Mr. Dark Jedi, Landon, and the Dark Jedi's two bodyguards, so several duels erupt- The NPC Bodyguard dies spectacularly, but the other one and the Dark Jedi escape, alongside Landon. The crew makes it off barely in time before Star Destroyer goes "KABLOOIE!"
Then, they get what they wanted from Dantooine (a Jedi Holocron that Risa, who wants to learn from it, and another crew member who wants to sell it for lots-o-credits argue about) and leave, heading for Nal Hutta to get rid of the Hutt who's got a problem with multiple crew members. They get in, kill everyone who's bad, and get out. They end up fighting their way out when power-hungry Hutts decide to cash in, and they barely escape. They then go to Mygeeto again, and leave. They get intercepted near Toola by an Interceptor Star Destroyer with the Dark Jedi on it- they have to land on the planet and hide the ship, then fight off Imperial Troops and hostile Whipids in the snow and ice. Fun. Eventually, they beat the Dark Jedi's forces off, and decide to deal with him. They follow him, but not before convincing a group of Whipid Warriors who are against the Empire to follow in two crago transports of their own. They arrive at Korriban, where the Dark Jedi is. They land, but on Whipid ship is shot down and it crashes into a temple, exploding. The crew and their remaining mercenaries get out and hunt down the Empire-occupied tomb of some long-dead Sith Lord; we'll make him up, too.
So they end up killing almost all Stormtroopers, alongside their remaining Whipids, who also end up mostly dying. Only the best fighter and one other make it with the crew to the Central Chamber. They have to fight a Sith Alchemy-modified Rancor, a mutated Acklay, and a Krayt Dragon in there, along with two Terentateks at others times earlier in the temple. Then, the Dark Jedi reveals himself, along with his Imperial Shadow Guard. The duels ensue again, as the Dark Jedi's last remaining Imperial Assassins, minor Dark Jedi, his Acolyte, and his last elite Stormtroopers fight against the crew and the two Whipids. The Whipids die, like good NPCs, and the stormies and other Imps all also die- excluding the Dark Jedi, his Acolyte, and his Bodyguard. The Acolyte is killed by Risa, and the Dark Jedi gets pissed. Then, all of a sudden, the Imperial Shadow Guard stabs him in the back. Literally.
He attempts to flee, and during the chase, he detonates several in the main hall, where the crew is still at when they're running. The pillars and ceiling fall, but everyone lives- one or two are injured though. The ones who can run to their ship as the traitorous Imperial makes it to his starfighter. The crew mans the guns, not lifting off, and when the Shadow Guard flees, he gets shot down. Boom. Dead.
They go back to the damaged Temple, and get their wounded, but have to fight Landon on the way back. They kill him when the Bith member of the crew shoots him multiple times in the back, because he had been injured earlier and was still hiding in the pillars, and Landon had his back to him. They get to their ship, but it turns out Landon survived- he breaks into the ship, captures a few crew members, but it eventually riddled with blaster bolts, but still surviving is blasted out of the airlock into space. The crew leaves to clean up the loose ends of one or two major crime lords, just so their crew'll be safe. Voila.
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That's my plot idea.
As for the bad guys, here's my idea:
We should have Spartan-777 control the most promising Dark Jedi, who Vader has been eying as a rival for some time. The Dark Jedi in question has two Shadow Guards to defend him, one being Jax Stellyn, the one I made a profile for. We will also have these crimelords against us:
(1) Yooba the Hutt- killed by Ara on Farffin
(2) Mekka'chek- Weequay pirate, killed on Rodia
(3) Jabba the Hutt- we escape from him
(4) Eego- Rodian male, killed by us on Coruscant
(6) Jeabba the Hutt- escape from her on Nar Shaddaa, kill her later to tie up loose ends
(7) Moraten'una- Twi'lek male, killed on Nal Hutta
(8) Nookoo the Hutt- Killed on Nal Hutta
(9) Moraka the Hutt- Killed on Nal Hutta
That good?