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Anyone know (from the script or book) why Anakin was crying on Mustafar after he killed the Separatists?

Same reason he cried after slaughtering the tuskens, that adrenaline died off. He began to think about what he did, at that time he wasnt totally lost.

he is just sad...too much has happened too fast...one day he is a good guy...the next say he is killing of people that he has lived with his whole lieft...

atleast that is what I think...

well there was some good still left in him....Padme said it Luke proved it...if anyone who just killed a bunch of toddlers and thought mission over after killing spermatists then takes time to reflect etc..i imagine they would cry

Conflict.. he has it in ROTS and still has it in ROTJ.. hence theline ' I know there is still good in you..'

He realized that he was way deeep in sh*t now...