Which of the characters instigates a rebellion against Napoleon in "Animal Farm"?
I suppose you are referring to the hens, who decide to go on strike for having their eggs confiscated. Their pseudo-rebellion (along with the sheep's) is thwarted, and there are inquests, forced "confessions" and even executions.
The real instigator, however, is the aged boar Old Major, who was the animal who convened the farm animals in the barn to encourage them to protect their rights as well as that of their posterity. Old Major died after his insurrection speech and therefore was not on scene upon the actual moment of the animals' rebellion. Nor did he witness Napoleon's rise to power and the reign of terror which followed.
As for Snowball, although he was accused of treason in Chapter Seven, there is no reason to think he actually did anything of the kind. As Napoleon's rival he was a threat (He was smarter and more inventive than Napoleon.), so he was simply chased off the farm by Bluebell's dogs, whom Napoleon had trained to be his secret police. Whether Snowball survived his expulsion and was really prowling around the farm as rumoured is never divulged.
The two prominent characters who rebel against Napoleon are the three young pigs and the hens.
Firstly, the three young pigs confessed that they were working and plotting with Snowball which resulted in their execution.
The hens however flew up to the rafters of the farmhouse and laid there eggs there because they didn't accept the contract that Napoleon had signed with Mr Whymper for 200 eggs per week.