The flood are the pirates of the game. They are non-playable. They infect everything which adds it to the floods growing army. They will take planets, ships, and more with ease. Every ship you can make is prey to the flood. Its is recommended to avoid the flood plants with any warship, use scouts, or any fleet with more than one ship. After the flood gets a big enough fleet it will start attacking planets. Then they will seem almost unstoppable and will take an entire star system.