What happens when I play Moonfall choosing an enemy unit while I control an empowered Mel, Newly Awakened?

The chosen unit will be given -3 [M]. All other enemy units at the chosen battlefield will be given -2 [M].

Mel, Newly Awakened’s empowered ability is a replacement effect. It replaces the event of a spell or ability you control giving a unit it chooses -[M]. The event it replaces that with is the spell or ability giving an additional -1 [M].

Although Moonfall gives -[M] to multiple units, only one of them is chosen, and thus the only event that is eligible to be replaced is the chosen unit being given -2 [M]. It will be replaced with that unit being given -3 [M]. The events of the other units being given -[M] will not be affected by this replacement effect.