The anime will feature an original story from the game on which it is based.

After recovering from the inner struggles he faced in the past, Daigo Shigeno continues to play baseball and is now the captain of Fuurin Private Academy Middle School's baseball team. Alongside Mutsuko Sakura, his classmate from elementary school, he aims to lead the team to glory. However, due to unexpected circumstances, Fuurin's baseball team is left with only six members: Daigo, Mutsuko, Yayoi Sawa, Tao Sagara, Seira Kandori, and Hiromu Tanba. Left with mostly female players and lacking in experience, the team struggles to gain confidence and trust from the new recruits—Akira Nishina, Anita Kabashima, and Chisato Fujii. Facing challenges such as having no proper coach, problematic recruits, and a limited number of members, Daigo's resolution is put to the test as he tries to bring the team together in time to participate in their first ever tournament. [Written by MAL Rewrite]

Jiyu Nanohana is an ordinary schoolgirl until she runs across a scatterbrained 300 year old samurai who tells her that she is the reincarnation of Yagyu Jubei. With the help of the "Lovely Eyepatch" she transforms into the legendary swordsman whenever she needs to use his awesome fighting ability, which she needs to do quite often as a rival clan is dead set on conquering Yagyu to satisfy an old family grudge.

The year is 2148. Two years after the end of the original Fafner in the Azure TV series, Tatsumiya Island and its surviving residents have returned to some semblance of recovery. However, things have become desperate for our hero, Kazuki; nearly blind now, and partially crippled from his battles with the Festum two years earlier, he clings to the promise his fallen friend Soushi made to him to return to the island and set things right again. Kazuki's hopes flare when a lifeform is detected within an unmanned submarine that comes floating into Tatsumiya Bay one night, but the person aboard isn't Soushi; it is a mysterious "boy" named Misao Kurusu who may not be entirely human, and who claims to have been sent by Sōshi. With Misao's arrival, hostilities break out anew between the Human Army and the Festum, and the Fafner pilots are thrown into the most desperate battle of their lives - this time, with the fate of TWO races riding on their shoulders. 

(Source: Wikipedia)