Because Bagheera's a coward! No, seriously I think it was because he got seperated from Baloo when searching for Mowgli. He only found Mowgli near the end of the fight because of coincidence. In the orginal story by Rudyard Kipling, it was said his ferocity and cunning win him respect of all the jungle inhabitants, except Shere Khan of course. However, I doubt that's why he wasn't included in the climax becuase the 2 stories are very different from one another. Maybe they just didn't know how to include him into the fight.
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