after shinji starts the third impact and everyone's consciousness melds into one another shinji offers everyone a choice, stay inside whats basically a heaven or come back to reality. when shinji's laying there in the dead world hes there for an indeterminate amount of time, alone. when asuka comes back hes probably mad with the guilt of ending the world and angry that everyone decided to stay inside heaven, as well as unhinged from days or weeks without any human interaction. its theorized that he started choking asuka to test if he was still dreaming or if he was in reality, cuz if he was dreaming asuka wouldn't react but if it were real she'd probably try to fend him off. her showing affection to him probably threw him off completely, its actually shinji calling himself pathetic, not asuka.