In the midst of an industrial revolution, the people of Hinomoto fight hordes of undead creatures, known as Kabane, using powerful armored trains. (Compilation film of the second half of the original TV series.)

Finally, the day of Mai's high school graduation has arrived. While Sakuta eagerly waits for his girlfriend, an elementary schooler who looks exactly like her appears before him. Suspicious, and for all the wrong reasons... Meanwhile, Sakuta and Kaede's father suddenly calls, saying that their mother wants to see her daughter. She was hospitalized because Kaede's condition had been too much for her to bear, so what could she possibly want now?

The story centers on a high school girl named Tamahi, who encounters strange creatures while navigating a gigantic apartment building.

Kotaro visits Komada Distillery for a project on Japanese craft whisky. Led by young female president Rui, who took over the family business, the distillery works hard to reproduce its signature whisky, Koma, which they had to stop making years ago. However, not to mention financial backing, too many clues are missing to revive the once lost whisky.

In a Holy Grail War, Mages (Masters) and their Heroic Spirits (Servants) fight for the control of the Holy Grail—an omnipotent wish-granting device said to fulfill any desire. Years have passed since the end of the Fifth Holy Grail War in Japan. Now, signs portend the emergence of a new Holy Grail in the western American city of Snowfield. Sure enough, Masters and Servants begin to gather... A missing Servant class... Impossible Servant summonings... A nation shrouded in secrecy... And a city created as a battleground. In the face of such irregularities, the Holy Grail War is twisted and driven into the depth of madness. Let the curtain rise on a masquerade of humans and heroes, made to dance upon the stage of a false Holy Grail.

While Rena and Maki recover from their injuries, the other SORD members jet off overseas for a school trip. Within moments of their arrival, though, the Mihama gang are pulled into a manhunt for a SORD deserter, assisted by student Sylvia and Velvet of St. Aile's International School. Tohka's the star of the show this time round, but she's wrestling with her own issues - old memories of her parents, and a promise to a friend that she wasn't able to keep...

Summary of the first season of the show, as seen from Rikka's perspective with new elements.

A young girl, from a civilization that resides in deep underground tunnels, finds herself trapped in an inverted world and teams up with a resident to escape and return home.