Theres nothing to understand. At the end of the day it doesnt make sence. Darko's job is to realign space and time after the artifact from the future falls into his time line (the engine), thats the point of the movie, realigning everything, but at the end, the engine still falls back through time, except this time Darko dies, so there is no one to realign time, and the universe ends. End of story.