In the skies over the ocean, human force jets take on a large number of Festums while life is peaceful as always on Tatsumiya Island. Class president Ryou Masaoka sends off new graduates as they leave the island. After, one of the graduates asks Ryou if he wrote the speech himself and he says that his vice president, Yumi Ikoma, helped him with it. The graduate accuses him of being lazy and tells Ryou that he should be sure to confess to the girl he likes before it’s his turn to go. Later, Ryou watches Kazuki and Kenji fight. He asks Soushi who he’s betting on but Soushi excuses himself. Ryou comments that Kazuki and Soushi always used to play as kids and Yumi says there must be a good reason for why they don’t talk anymore. Ryou asks Yumi if she’d look after his dog, Puku, when he graduates and she yells at him, saying he should take Puku with him. Ryou says he has something to do and greets Karin Kuramae on his way out. Karin wonders why he’s leaving early and Yumi says he’s heading to the hospital. Yumi says they need to be on top of things because Ryou is lazy. Ryou rests under a tree, unable to move until Kazuki finds him and helps him to the Toomi clinic. On the way Ryou tells Kazuki he needs to approach people to become friends with them, but adds he has no right to say that because Kazuki is helping him. Shouko is already at the clinic and is surprised to see Kazuki. Kazuki leaves and Ryou asks Shouko if she’s there for a check up. She says she wasn’t able to go to school that day and comments on sicknesses being genetic. Ryou says he has the same sickness as his mother and Shouko wonders if Houko is really her mother. Ryou says he’s envious she has such a caring mother. Shizuru says Ryou’s gotten better and he asks about what he volunteered for. He says he wants to do something before he dies. Shizuru asks if it’s tough living alone and Ryou says since it’s a small island, there are lots of people to look out for him. Ryou leaves and sees Shouko petting Puku. He asks why she’s not going home and she says Maya will be back soon. He says he’s envious that she still has close friends while most of his graduated. She says she’s envious because he’s popular and the class president but he says he was forced into the position while he was away. He says he’s glad they didn’t forget about him and Shouko thinks they’ll forget about her. Maya walks up and Ryou says Shouko needs to cherish the friends she has.
Yumi arrives home to find her bedridden father with Fumihiko Makabe and Kouzou Minashiro. Her father hides data for Plan L and the Fafner Titan Model and Yumi offers their guests tea, but they say they’re just leaving. Yumi asks her father why there are so many graduation ceremonies and wonders if it was like that in his day. The Alvis board meets and talks about a group of Festum nearby. Fumihiko says they can’t engage them because the core isn’t fully developed. They review Plan L and some are outraged about using the children. Kouzou says they need everyone’s approval. Kazuki and Soushi awkwardly pass each other in the hall and Kenji once again challenges Kazuki. Yumi tells her father that she’s meeting a friend at the beach the next day and would try to be back early. Yumi swims in the ocean while Ryou watches from the beach. She asks if he’s going to swim but he says he’s lost confidence after watching her. She asks about his health and he says it’s fine. Yumi thinks she understands what it’s like because she has to take care of her father. Ryou gets up and says he’ll go for a swim and that he’s never thought he needed caring for. Yumi grabs his hand and apologizes for hurting his feelings. She says she had fun and was able to forget about her father for once. Yumi returns home to find her father collapsed outside. Before he dies he says he needs to go to Alvis. At the funeral Yumi asks Soushi if he knows what Alvis is, but he says no. In her yard, Yumi finds her father’s handheld and sees the data for Plan L and the Fafner. An Alvis keycard pops out and Yumi hears her father’s voice in her head. He says to go to Alvis and enter the L Boat hanger. She finds her way to the Fafner hanger and is met by Karin, Soushi and Ryou, who congratulates her for graduating. On an Alvis train, Yumi says her father’s voice has been in her head the whole time and Ryou explains it was memorized information taking on a voice. Yumi deduces that everyone who finds out about Alvis ‘graduates’ and Ryou says once they find out, they can’t return to a normal life so they choose to fight. Ryou says he stayed behind because he was waiting for Plan L that Yumi’s father created and Yumi says she didn’t know anything. On the surface Yumi says her father must have intended for her to take part in the plan and Ryou says she doesn’t know anything. Yumi snaps and asks if he knew everything the whole time. She says she doesn’t want to be with Ryou because part of her blames him for her father’s death. Ryou gets his orders and is glad he can repay the people who gave him a place to belong. Yumi decides to volunteer and cuts her hair.
The pilots gather and Ryou is surprised to see Yumi there. They are briefed on the plan which is to detach a part of the island and send it adrift and defend it, fooling the enemy into overlooking the real island. The pilots begin their VR training and Ryou runs around, happy he can run so fast without running out of breath. Yumi falters and is briefed about crossing. Ryou is her crossing partner but she refuses and asks for another. She is told it is to maintain balance and Yumi feels Ryou’s sense of joy. The sim’s time runs out and they are told about the Fafner’s assimilation phenomenon and that is might lead to their deaths. Ryou tells Yumi she should quit and she says he should because he has no intension of returning alive. There are eight pilots to four Fafners, so they practice a shift system. Some pilots try to feed Puku, but Ryou says Puku only eats what he gives him. They can’t take Puku with them, so Ryou puts poison in Puku’s food but kicks it away before Puku can eat it. Karin sees Puku in the Alvis hallway waiting for Ryou, so she offers him a snack. Soushi and Ryou talk about the new model Fafner and Ryou is shocked to see Puku eating from Karin’s hand. Ryou leaves Puku in Karin’s care and the L Boat departs from the island. Soon after, they are attacked by a Festum and Yumi and Ryou launch. They struggle, but eventually destroy the Festum. Back on the island, Karin and Soushi do tests in Fafners Mark Ein and Mark Zwei but it doesn’t work for Soushi because of his eye. Back on the L Boat, Festum continually attack and some one is killed. After the sixth battle, pilots start succumbing to assimilation phenomenon. Yumi requests that combat time to shortened to 10 minutes to prevent pilot exhaustion and the commanding officer asks if her father told her how they’re supposed to escape at the end. He suggests there isn’t an escape plan and Yumi says her father wouldn’t sacrifice them all. Ryou says that they should trust Yumi’s father and agrees they should shorten the time. The next day Yumi thanks Ryou for standing up for her father and he apologizes. Yumi says she knew he wanted to die because she felt the same thing she did with her father. They are called to the lobby and told a new part of the ship, loaded with supplies has opened up. Because Festums can read minds, details were hidden from the crew and revealed on a timer, so the escape plan will be revealed at the end. Soushi stands in front of Tsubaki and remembers Kouzou telling him he will operate the Siegfried system. Soushi asks how many people are expected to survive the mission and Kouzou says the estimate is low. He asks Tsubaki if he’ll be able to carry his burden. The battles rage on aboard the L Boat and one of the Fafners is permanently disabled and more pilots succumb to the assimilation phenomenon. Finally, some pilots turn into crystal and disappear completely and the remaining ones loose hope. One more Fafner and pilot are lost in the next battle.
Back on the island Soushi remarks that Karin’s now red eyes are a symptom of assimilation phenomenon but her special glasses turn them back to green. She says it must be nothing compared to what Ryou is going through and that she wants to tell everyone what’s happening. Soushi says that would nullify what they’re doing. On the L Boat, there are only 2 Fafners remaining and 3 pilots. The timer runs out and the path to an escape sub is open. The enemy appears and Yumi and Ryou launch to fight them. The others board the sub and notice that Fenrir is activated. Yumi and Ryou take out a few Festums before retreating and the L Boat self destructs. Alvis detects them and Karin launches to pick them up. Festum, who are discovered to be able to go underwater, surround the sub and destroy it. Yumi tries to go back to the island but Ryou stops her, saying they can’t lead the enemy back there. They head away from the island and Kouzou orders the mark Zwei to stop. Karin won’t listen so Soushi has to lock her Fafner. She begs him to let her go and Soushi tells his father they could get valuable data if they got the pilots back alive. Kouzou gives in, but limits Karin to their defensive perimeter. On the ocean floor, Ryou calculates the tidal data that will bring the wreckage back to the island. Yumi thanks him for stopping her as Fenrir ticks down. Ryou tells Yumi he loves her and she says she’s not sure what she feels about him. She asks if what they did will reach the island and wonders if her father would praise her. Snow starts falling and Yumi asks how it can snow underwater. Ryou says it’s marine snow and that everyone must be praising them. Yumi says she’s glad Ryou is the one beside her and wonders if that means she loves him. She’s about to say something else, but her body crystallizes and she disappears. Ryou records a final message about their fight and his body starts crystallizing. A Festum appears and Ryou realizes that Festums have lives of their own. Fenrir activates and Ryou is killed in the explosion. The shockwave reaches Tatsumiya and Kouzou realizes that the Festums must be able to go underwater. Soushi orders Karin back to base and she weeps. Four months later a Titan model cockpit washes up on the island with all its data. Karin and Soushi wonder who piloted it and Puku runs up and climbs into the cockpit. He sniffs around and starts howling. All the Alvis members on the island weep as their hear Ryou’s recording. Karin finds Puku in the cockpit again and tells him he was right about it being Ryou’s cockpit. She says he was probably with Yumi until the very end. When she pats Puku’s head, she realizes that he’s dead. She starts crying and says he’s a good boy for going to his master’s side. Karin prepares to leave the island and intends to return early and Soushi says Solomon predicts that Festum will come to the island soon. Karin wonders if their friend’s battles were significant since it was only peaceful for half a year. Soushi says they are always living in a peace won by others and that he’ll be thankful for even a day of peace. Karin says she’ll wait for the day when they can fight together.
After Fafner’s fantastic finale we are treated to a prequel, and what a treat it is. Going in one must realize that most of these characters are doomed, for they didn’t appear in the original. Ryou is a unique kind of pilot, one who has no objections about doing what he’s doing and is a pretty laid back guy even in the hell he’s been thrown in. Yumi is also a likeable character and her relationship with Ryou is touching, but alas it ends in tragedy. Even Karin, who survives this special, dies in the first episode of the original series. One must admire the bravery of L Boat’s crew. Even from the outset the plan seems hopeless but they manage to succeed even at the cost of their own lives. Some joy can be taken in the fact that since it’s a prequel, some characters that died in the original appear like Shouko and Kouzou. The battle scenes were choppy at best, jumping right into the middle of the action and ending a few seconds later. Action fans will be disappointed, but the action is not where the story lies. This special captures the emotional character drama from the original and truly lives up to the Fafner name. This is a great special for Fafner fans and newcomers alike.