At the end of season 5, Mother's Mercy. Jon Snow is killed by a group of Night's Watch "rebels" or group of Night's Watch that didn't agree with Snow's decision of bringing Wildlings in the Black Castle.
What I do not understand is the reason they killed Snow and their timing as well. If they had an issue with wildlings they shouldn't have lifted the door to let them in as we see in Hardhome, I thought that will be the most important scene of season 5 because for a moment it seemed as if Ser Alliser Thorne is not going to permit Wildlings to enter. But we see Wildlings peacefully enter Black Castle. If they had a grudge against Wildlings they shouldn't have let them enter in the first place. But once they have entered, what is the reason to kill Jon Snow, knowing that he is the Lord Commander and an expert swordsman and considering the fact that they are on brink of war with White Walkers, it doesn't make much sense.
It seems as if Jon Snow's murder was not only because of Wildings but because of Ser Alliser Thorne's grudge with Snow as well. If I missed something kindly explain.