Jonas and The Guild
I am starting to suspect that Jonas Sr. was Force Majeure. All these pieces here and there seem to vaguely fit. He was likely killed by, or deposed by The Sovereign, or perhaps just wanted to retire anonymously and handed the Guild over to him. The Sovereign even briefly took on Jonas' form in ATAG2.
* We always see him and Team Venture battling members of the Fraternity or Torment, not Guild villains, and the FoT was a rival organization of the Guild.
* The Monarch's dad / Blue Morpho (I don't think he's on OUR side)/ Venturion / Vandata. The "plane crash". Kano's confession about taking from the world a great man. Kano Joining Team Venture. Col. Gentleman - "Don't believe everything you read in those comics." And we haven't heard the last about the baby killing either. They can't just drop it like that.
* The Monarch can't remember playing with Rusty as a child.
* Doc probably doesn't remember playing with young Malcolm either, and maybe that's why Doc also didn't remember Hector (not just because Doc is dick). Memory wipe or alteration likely.
There is something very sinister going on. Jonas probably played at being a "good guy" in the public eye but behind the scenes he ran the Guild of Calamitous Intent. And he might come back!