While Chrono Trigger (1995) usually takes days to complete, Crono decided he'd rather not have to sit through all the unnecessary stuff, like long cutscenes, unskippable boss fights and key plot events, so he did it in three minutes instead.
The 18-minute improvement comes from utilizing mid-frame resets which were recently implemented in lsnes.
Reading the authors' comments is a requirement if you want so much as a clue to what's going on.