You're missing the fact that grabbing skulls in multiplayer makes the player stronger, unless the rules are changed. Collecting skulls in singleplayer will add various effects, like additional humourous dialogue, making enemies throw more grenades, making all enemies captains, etc.
For a second, I thought this was Groudon from pokemon. It makes sense, at least, that he would want to repel a "flood"
The Flood are a creepy as alien zombie race from the Halo series. I love pokemon too, but fuckin dod gammit! There's more t' life than dat dere pokemons!