freelyx

If she's doing this cyber-manipulation on Spencer in order to gather information for a media newsgroup and her blackmail enterprises, it occurs to me that should could be planning cyber-manipulation of dozens of people. If the cybernetic upgrade that Spencer got is fairly common among accountants and advisors, she could eventually build a vast network of backdoor information.
 
Of course at that point, she would be unable to personally look at all the information and would have to depend on flunkies to do it for her. Heck, she probably would be able to personally sift through 24 hour surveillance of just Spencer.
 
I could see some surveillance-processing underling noticing that the mastermind is making millions then look at his own paycheck and decide he'd be better off using some of the information to make millions himself. The mastermind might be good enough to completely cover her tracks in stock market manipulation or blackmail schemes, but an underling going into business for himself for the first time might be clumsy enough to draw attention to himself.

Ooooo, some valid points and interesting possibilities here.  Tech is something that can be hacked and Spencer, while cutting edge and well defended, would not be "perfectly" covered.  I like the idea that he is being used, although maybe rather than being controlled, he's just got some form of monitoring software installed that is reporting to "X" whatever information he gets.  They know he is trusted by Rogen and is using that information to their advantage by listening in or watching unnoticed within his system.
 
I also like the idea of the savvy enemy being something a little more to Rogen than just your everyday rival.  I think maybe the enemy is female, perhaps an ex-lover or relationship Rogen has long since forgotten.  An incredibly brilliant all be it jilted ex who thought she'd be the one to take Rogen out of his hedonistic lifestyle and get the eligible rich bachelor to settle down with her.  Now she's making millions behind the scenes stealing his business ideas, contacts, and getting him manipulated into hot water with his other known associates and these legal problems are really just a distraction to slow him down so she can get the leg up on his company. 
 
She can be his Lex Luthor, to smart to be directly implicated in the criminal aspects of whats going on, working behind the scenes as the puppet master to sully his reputation and build herself up as his viable replacement.  She should have decent security, maybe is linked up with one of the PC's hunting militia groups.  Then grant her lots of social and political pull.  Maybe have it be manipulative as well.  She's got dirt on people that don't want it getting out in the public... Maybe she owns a media newsgroup... Yeah, I like where this is leading.

You have basically four avenues of ideas to explore
 
1) someone is after Rogen
2) Spencer is deliberately screwing over the boss
3) The aliens who were "accidentally kidnapped" weren't kidnapped accidentally at all but wanted to be there
4) Rogen is guilty
 
1) someone is after Rogen - almost all motives come down to sex or money
ex-wife
ex-business partner
business rival
romantic rival
relative or friend of someone Rogen squished along the way to power
vigilante who couldn't figure out another way to bring Rogen down other than to set him up
 
 
2) Spencer is deliberately screwing over the boss. (One a side note, was that really the best craft Spencer could have procured?)
Rogen screwed Spencer's wife
Rogen has been underpaying/under-appreciating Spencer
Spencer is a lunatic
Spencer thinks he can take over the Rogen's whole business
Specer has been embezzling but he's in so deep that getting rid of the boss is his only way out.
 
 
3) The aliens who were "accidentally kidnapped" weren't kidnapped accidentally at all
The aliens needed transportation and stowed away. Maybe criminals or political refugees. Maybe working a business or political deal. Maybe they assassinated someone (slowly) and got a free trip home: how much radiation can they emit anyway?
The aliens' plans were unknowingly foiled by Rogen so they want revenge on him
The aliens wanted to see human technology up close. Maybe the ship malfunctions were due to the aliens experimenting with controlling ship systems. Prelude to invasion or maybe they just fiddled with whatever defense systems or commerce systems they found along their round trip. Seems like they might be great spies for their own civilization or for another.
The aliens wanted to examine another solar system up close to find a gas giant or two to quietly colonize.
Were there only three aliens kidnapped or might there have been more and one was deliberately left behind? Is anyone completely sure the envoy is coming alone and doesn't have an invisible friend?
 
4) Rogen is guilty
Rogen kidnapped the aliens to examine them and try to find an easy way to exterminate their race.
Rogen got some kind of ransom on the side which was worth the legal troubles he's in.
The aliens themselves are a valuable resource which could be enslaved to power devices or ships cheaply. Or perhaps leave a residue behind which is useful. Or their energies can transmute matter when they're agitated: how much of the most valuable substance in your universe could three of them transmute in their few days/weeks of captivity? And what is the most wild thing that substance could possibly do?

Maybe Rogen was being set up? The energy beings were planted where they were specifically to get Rogen in trouble and allow Entity X to take control of his operation. Naturally, X will try to prevent the misunderstanding from being cleared up. OTOH, once the mission is completed, X will ignore the PCs (from his perspective, they're just hired muscle).