*SPOILERS*
Hm... judging by the intro to this game, the ending of this game, and the ending of MS3...
I think we may be meddling in split timelines. And perhaps... there will be a timeline where Dregg didn't kill Arc somehow?
I think I've found all 6 secret upgrades. Two in Mission 0, one for beating Mission 100, one unlocked somewhere after Mission 36, one for each form of the boss (two total).
I feel so smart. The bluetonium was out of my reach, so I activated my Blue Force Generator, let it move around and the generator to run out, then I grabbed it.
The only way to survive depleted bluetonium is with the bullet jumper upgrade and the blue force generator active (which also makes depleted bluetonium hurt enemies FYI), but only if it can move away from you. Luckily by the time you have to deal with it you have plenty of upgrades so you can dodge it pretty easily - and when you can't the portal generator can be used to teleport it away from you.
 "Medieval Chronicles 2"){kind=icon}
 "The Company of Myself"){kind=icon}
 "Feed the King"){kind=icon}
 "Medieval Cop - Adam and Eva"){kind=icon}
 "Realm Grinder"){kind=icon}
 "AdVenture Capitalist"){kind=icon}
 "Multitask"){kind=icon}
 "Accelerator"){kind=icon}
 "The Idle RPG 2:Renicipation"){kind=icon}
 "Cosmic Clicks"){kind=icon}
 "Run 2"){kind=icon}
 "Goodgame Empire"){kind=icon}
 "The Idle RPG"){kind=icon}
 "Saturn Blue"){kind=icon}
 "Coinbox Hero"){kind=icon}
Not quite, there is only 1 secret upgrade from the boss. The other secret upgrade is from the *spoiler alert* practice level.