At Anime Expo 2017, Production I.G. announced that the long-awaited second and third seasons of FLCL will air in 2018. While a concrete release date is not confirmed as of yet, both the second and third season will follow the same format as the original and contain only six episodes each. FLCL 2 and 3 were originally scheduled to air this year; however, they stated that they decided on a 2018 release instead. They also said that there would be a break in between both seasons, rather than running them back to back.
Adult Swing describes the story of FLCL 2 as follows:
In the new season of FLCL, many years have passed since Naota and Haruhara Haruko shared their adventure together. Meanwhile, the war between the two entities known as Medical Mechanica and Fraternity rages across the galaxy. Enter Hidomi, a young teenaged girl who believes there is nothing amazing to expect from her average life, until one day when a new teacher named Haruko arrives at her school. Soon enough, Medical Mechanica is attacking her town and Hidomi discovers a secret within her that could save everyone, a secret that only Haruko can unlock.
But why did Haruko return to Earth? What happened to her Rickenbacker 4001 she left with Naota? And where did the human-type robot ‘Canti’ go?
In addition, FLCL 2 is going to have a manga adaptation, but no publish date was revealed just yet.
Japan will get both seasons in a special way as they will be airing in Japanese theaters! Streaming services here in the United States will still treat the show as a standard television anime, though.