Bass is the one responsible for kidnapping Dr. Wily and stealing his robots.Just think about it: who else would go through all the trouble of doing all that? When you consider that Bass didn't get the chance to fight Mega Man for a while, it seems pretty logical that he'd have to do something pretty extreme to get his attention. So what better way to do that than taking over Dr. Wily's army of robots and cause a world-wide rampage? The proof is there, too; in the older version of the intro sequence, Wily's kidnapper's eyes are shown near the end of it and they're red (which, of course, happens to be Bass' eye color), not to mention that he's clearly goading Mega Man into stopping him. Finally, he is present on the game's official cover and has a bigger presence than everyone else on it.
The identity of Mega Man's rescuer in the endingIt couldn't be Proto Man due to his ending monologue. He hopes Rock "escaped"? That doesn't sound like someone who just carried the guy off to their creators' Lab. "Survives" would have been the term used if that were so.
On the other hand, Bass was also at hand, and is the only logical alternative (with Wily carting off Zero). In fact, his ending monologue sounds like the fruits of a Mistreatment-Induced Betrayal.
The reason Rock was inmune to the virusit's because of Duo, According to Mega Phil X, the game takes place any time after the events of 7. It was originally going to occur after 9, and just like in 10 the reason behind the robot rebellion is because of a virus, it's possible that both viruses are derived from MM 8's evil energy, at the end of that game, megaman was attacked by the evil energy, and then saved by duo, this contact while he was purifying him somehow made him develop some sort of antivirus program that was adaptable enough to resist the variatianos created by willy, alternatevly, Dr. light was able to obtain some residual data from that energy and he developed the antivirus himself and installed it on rock in case he would need to face a similar treath, since protoman doesn't fully trust Dr. light to let him mess with his inner circuits, and roll is only a household robot not intended for combat, just like most robots around the world, they weren't vaccinated and therefore still vulnerable to the Zero Virus/Roboenza, and since Willy was trying to amplify the effects of the evil energy, it probably wasn't in his initial plans a way to damper said virus, making his robots just as vulnerable