I don't think Isis is bad. I think she's just motherly and wants to protect her son and also Anubis at all costs. Osiris is the one pulling tricks
Comment by Netana on Ennead - Chapter 38
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To add to that, she might also be blinded by her love for Osiris, which in return blinds her to the idea he can do any harm to anyone and since Set killed him, she can't help but view him as her enemy.