1) In biblical terms, The Flood is essentially an apocalyptic event in which Noah, the only man meant to survive a worldwide deluge, takes 2 of each animal on an ark to avoid the complete and utter distruction of God's creation.
2) The "weapon" in Halo that The Covenant was in desperate search of acquiring in order to wipe out mankind (NOTE the similarity between this and definition 1.) The Flood itself, is actually a humanoid, body-snatching race of fungal origin and consists of 4 subtype species. Can easily be n00bed via shotgun.
"I just learned about The Flood in Sunday School."