This is story related and unmissable BUT you must be doing the Red/Moral path to get it.
Omegamon (aka Omnimon) is an Ultra level Digimon (Ultra is a stage above Mega and is the only one of its kind in the game), is absolutely the most broken Digimon available, and is a fusion of
so you will need to be doing the Red/Moral karma route but NOT doing the True Ending route.
The best way to avoid the True Ending route is to let
die and continue on as normal.
In Part 11 you'll get a cutscene where the fusion begins and once you see it the trophy will pop.