Okay, this is far more than a theory, speculation or random thought. This is a revelation. At least that's what it hit me as. Most theories stem from only one episode, maybe two, three at the most. This conclusion about the Farscape Universe I've gleaned from ABL, the S1 Finale, a teensy bit of LATP, ACN, and LGM(specifically part 2-3). I ask you to bear with me as I describe this Universe I've managed to see when considering the information presented in all of these episodes.
Remember what Larraq was carrying on his way to the Gammak base before the crew of Moya stopped him? That critter/virus thing that stealthily infected several people. Now why would he be heading to Scorpy's Gammak base, out in the middle of nowhere (actually kind of close to Nebari space, since they're in the UT). Neither Scorpius nor Jarveel had any idea they were coming. This I will attribute to extreme PK secrecy. The Gammak base would learn of the project when Larraq arrived. You see, PK Intelligence must have been either thinking along the same lines as their Nebari rivals, or they knew what the Nebari were up to, and decided to take similar action. What I'm talking about is the Nebari plan to frell the Galaxy with their timed virus. This is obviously a huge threat to the Scarran Imperium, the PK's biggest customers. It's also a threat to PKdom. Naturally, they're gonna fight back.
Meanwhile, on the Gammak Base, Scorpius is researching wormholes. Fervently. This was also top secret. Probably another aspect of the same master plan. Gilina didn't know what it was they were developing. She did assume it was a weapon. Remember in LGM3 Scorpy described how significantly the balance of power would sway in the direction of the one who possessed wormhole technology. Imagine, PKs using wormholes to send virus-laden ships to as many vital Nebari worlds as possible. Oh, the carnage.
For some bizarre reason, the (supposedly superior) Scarran Imperium actually values the allegiance of one puny Sebacean breakaway colony? Why? Three words, my friends: Location, Location, Location. These folks are in the UT, and probably a lot closer to Nebari borders than Sebacea Prime. Could it be that they are trying to marshal all the help they can get?
Remember also that Scorpius was playing around with Stark, a stakar attuned to the dying. It became apparent in LGM2 that Scorpius valued the powers of a stakar. Now, whether this was the sensitivity to death or something else, I really don't know. This may have been meant to couple with his own use of wormholes. Scorpius, I think, had his own plans, separate from those of PKdom or of the Scarran Imperium. This sort of blurs what we can learn from Scorpius, since he is so frellin' devious. Since it was Scorpius alone who mentioned in passing how it would have been nice to have another stakar, we can assume it's independent from the Scarran/PK master plan. I've mused before that Scorpy may have intended to use a stakar as reconnaisance with his wormholes.
And, um, we have seen that both Scarrans AND Sebaceans resent Scorpius' existence. He has no allies whatsoever--except the ones operating a rather suspicious Shadow Depository, where Scorpy had had a considerable amount of wealth stored. Now that those friends of his are gone (and they may not have been his ONLY friends), where is he going to go with that new found wormhole technology now that he has it?
Scorpius has a few options, and this is where my theory gets really scary. He could:
1) Join the Nebari and give the technology to them, because with all the connections he has, he knows the PKs don't have a snowball's chance in hezmana. If he does this, Scorpius becomes the most powerful supervillain in history and goes immediately on Your Phantom's BAD BAD MAN LIST!
2) Go to whatever allies he has left hidden in the UT (they could be ANYBODY) and use wormholes to beat the dren out of BOTH the Nebari and the PKs. Then the Scarran Imperium as a bonus. This would put him on Your Phantom's RATHER CREATIVE BAD BAD MAN LIST.
3) Something else. (I mean really, can we predict this stuff with 100% certainty?)
At any rate, the crew of Moya has pulled the strings in favor of the Nebari, but Neri & Co. might overthrow them anyway.