My question is assuming the flood is used by a flood survivor or evil antediluvian, can you negate The Flood or is it removed from play and therefore not targetable by a negate when the opposing player would have special initiative?
The Flood
If used by a flood survivor or evil antediluvian, remove this card from the game to discard all cards in the field of battle (except flood survivors) and all evil cards in play and set aside areas.