Secret Empire certainly doesn't lack for scope. This is one of those event comics that really does extend into every corner of the Marvel Universe, from superheroes to supernatural figures to cosmic empires. The only down side to that massive scope is that it takes a while simply to arrange all the pieces on the board. That's a problem Secret Empire #3 runs into. With so much emphasis on introducing new characters and conflicts, there's precious little room to build on what the series has already introduced.
The main, overarching conflict of the series is actually pretty straightforward at the moment. As this issue establishes, both Hydra and the Avengers are desperately searching for the scattered fragments of the Cosmic Cube, and both seek to restore the world to the way it once was. The main differences being both sides have drastically different ideas of what "it once was" actually involves. But straightforward though that conflict may be, the sheer number of rival factions and new players cropping up is getting to be a bit much. This issue especially suffers from two late-stage additions that threaten to bog down the series rather than truly enrich the core Hydra/Avengers conflict.