Rogue and Rebel are alternate versions of each other
There names are synonyms, they are unlocked in very similar ways(beating and sitting on the throne and beating throne 2 and looping) both have an affinity for portals(portal strike and healing threw portals) both are rebels from one of the major villain factions(I.D.P.D and bandits) both were very close to the boss of there respective faction(Lil Hunter and Big Bandit, whos names mirror eachother) Rogue was even given one of Rebels old ability, its also possible the other I.D.P.D members are all alt versions of are mutants(Grunt=Fish Inspector=Eyes Shielder=Crystal) with the Captain possibly being the Proto-Mutant/The Throne itself(similer diamond patterns can be seen on the captains helmet and desk as on the throne and the proto Statue, and the big blob she controls resembling a guardian.
The titular Nuclear Throne is a radiation-powered device capable of altering reality, specifically as a countermeasure in the case of a nuclear apocalypse.
Sometime before the apocalypse that led to the current state of the game's world, a group of scientists created the Nuclear Throne as a means of repairing the world via having it be capable of changing reality itself at the demand of whoever sits upon it, with its fuel source being radiation on account of how plentiful it would be post-apocalypse. This is why The Palace is entered directly after The Lab.
The reason why it seems to be both sentient and hostile to anyone who attempts to sit on it? Well, you can't just have any old mutant sitting on the throne! The intent of its designers being that if someone HAD fought all the way to the throne and managed to defeat it in battle, surely they would be able to use its power for good.
Throne II and the resulting loop is caused by damage to the throne's generators making its powers go haywire, altering itself into a truly living organism. Its destruction results in time looping back around to before the throne was destroyed...albeit with some quite obvious changes. With that being said, it's no wonder why the I.D.P.D. seem so focused on trying to stop the playable mutants from reaching the Nuclear Throne.
