I use a strategy here that minimizes the risk of being hit during this fight. There are two phases; however, during both, the player wants to remain behind Amygdala to try and force him to do his jump attack. During the first phase, you'll want to begin charging your primary attack as soon as Amygdala jumps. He will land on top of you and you will be able to attack his head. At some point you'll be able to perform a visceral attack on his head. After that point, he will eventually move to the next phase of the fight where he will begin jumping forward rather than straight up. Be careful here, remain behind him and attack the back of his arms for maximum damage.
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