To me this is just not a normal patron to get into trouble by, it's just too high powered.
Just the sort of thing that might get a Junior Agent of the Imperium activated, since it's world busting tech.
The minute most players know what is going on, they are gonna shove him out the airlock or figure on how to barter him away, with tremendous risks they will just be shot rather then paid off (know too much, traitor/enemy to X polity, etc.).
So a big key is they get clues but don't really know what he is.
I'd start with reports of mysterious deaths at a research station several weeks previous as a typical weekly news/rumor the players often blow off.
Then the scientist shows with his laughably cheap escape payment. If he's smart and financed enough, he would charter the ship for immediate takeoff.
Stays ahead of the information wave, no record of conventional ticket purchase, players are happy for the moment.
Scientist gets to next destination, warns players it is in their best interest to say he was never there, disappears, and all seems to be just a quirky quick payday with criminal overtones at most.
Then the various spy groups start showing up as the trail leads to the players.
Fun part could be that they don't show up as just Imps or Sols or Zhos or hey go wild even Hivers, but as disguised ops so the players don' t even know it's a high stakes game.
A lot would depend on what they choose to tell to whom. Dangerous as some might conclude it's best to off the players so the trail goes cold for the competition.
The Vegans enforcing their autonomy or even onto the game would be good deus ex machina to keep the players from being whacked. The various interested parties would not want to explain what they are really there for or why they are after the players.
Endgame for this could go several ways.
The players could decide to go after him once they know the truth for a big payday- or have one of those space noir moments where maybe they decide to 'do the right thing', which may involve something crazy or killing the scientist so no one else gets it- or make sure everyone gets it.
The Vegans could be bestest buddies if the players cooperate- or maybe there is a militant faction that now wants the superweapon for Vega.
Finally, this could all be a Hiver manipulation to get all the humanspace races to forego creating such horrors.
The scientist being convinced to go against his polity is their doing without his knowledge, and they are helping him with financing and their superior computer skills/equipment towards an end to publicize or horrify all involved to not proceed with development.