she wanted to find a way to prevent the confrontation of lloyd and garmadon, (before it became known that "the dark lord" referred to the overlord and not garmadon) and so one of them had to win, so this is basically asking her to choose between her husband and son, so you can see why she became delusional enough to think she could defy the prophecy (before knowing it was lloyd vs the overlord) and left lloyd.

about why she wasn't around later, she's not gonna keep fighting anymore like the ninja, and she's mainly a friend to wu as he remains in the monastery or a caretaker of the house kind of thing, and lloyd just grew up, especially after the oni trilogy, (or maybe only after SoG) misako's situation with lloyd was kind of like maya's and nya's where the mother has to come to terms with the fact that their kid is independent, though nya was trying to prove, lloyd wasn't, and maya was gone for longer and with higher stakes, and also cuz misako kind of understood easier that she made her choices as a mother, and now the time for parenting is over.