With out knowing what type of faucet it is it's hard to give you an exact way to fix. But it's clear the stem came unscrewed with the handle so you need to get the handle off the stem and then reinstall the stem I attached a generic videos of stem replacements but it would be better to know the name brand of faucet and look up specifically
Pretty sure that is an American Standard Aqua seal.
The rubber cup that snaps onto the end of stem is missing.
I see you got the seat out
If you can get the handle off the stem,
then just install a new stem assembly and a new handle if you find one.