I just liked the idea of having a professor as the crazy antagonist but ok :P I do like the idea of having other higher ups as well, it could also add more potentials like what they plan after Ragnarok is failed and the world is saved by Jett and Tyra.
And about the true intentions of the Ragnarok government-wise, mabye having some inner circle of higher-ups and not just one doctor as the plotters?
I still think that the Ragnarok should be something world-wide and not just the Valorian States, but that's just my opinion.
Awesome idea :D maybe we could have it like... the proper threat was mortally wounded and had to become part machine to survive making him mentally unstable and blames the world for his injuries? I hope that's not too general :/ also I would like to point out that I find it unlikely that an organisation would want to destroy the world, I mean what would be the point in destroying the planet? It would end their lives too (unless they have a failsafe or a way to escape the apocalypse?), that is why I like the idea of having a couple of high up people but maybe not a whole organisation devoting themselves to the end of the world.
final showdown between the boss and jett rerveals he's a cyborg too !? (gasp!) that could create a dramatic story ending. plus it would leave the option open of making the government officials omeone close to him/tyra who betrays them. eg. maybe jett's foster mum is the big high up government official?