Renton Thurston is the son of two scientists, and Eureka is a mysterious girl who can't live under the sun. They are raised together almost like siblings and become best friends in their hometown Warsaw. Right now, humanity has been at war with the Eizo, an alien life form that mysteriously arrived on Earth, since 2009. At six years old, Renton is the owner of a Larva Nirvash, who he only understands, and Eureka, who has no family, is cared for by his parents.
They also become close to Professor Dominic, who takes them up on the hill to witness a snow moon flower's bloom and explains that it can make their dreams come true, and when that happens, the flower will have the color of a rainbow. The professor announces that he is leaving and asks the children to watch the hill in case they see another flower bloom. He gives them the seeds of the flower as a farewell present and tells them that the seeds will help their dreams come true.
A week later, the professor dies in a military experiment to uncover a way to destroy the Azo. In her room, Eureka is scared of what will happen to her because she has been in the military's custody for as long as she can remember, but Renton assures her that everything will be alright and reminds her of what Professor Dominic said about the seeds. Suddenly, soldiers burst into her room, pull her into the light which damages part of her face, and take her away as she pleads for Renton to help her. Saddened to see her be taken away and enraged that he was too scared to do anything to help her, Renton vowed to find her no matter what.
Eight years later, in the year 2054, Renton, now 14-years-old, enters into the military as a child soldier and is soon assigned to the Independent Youths Unit 303 of the First Mobile Forces thanks to his exceptional performance as an LFO pilot, alongside with his Nirvash, and is promoted to Corporal. On his first mission, he is assigned to help his commander, Holland, retrieve the military's top secret project. However, during the mission, they encounter dozens of Azo, and while fighting against them, Nirvash moves on its own and crashes into a nearby building, where Renton discovers Eureka. Equally shocked to see each other, he asks her to come with him so he can get her to safety but she refuses because she doesn't want to get him involved in her issues. After berating her for deciding to reject his request to let him protect her, he then rescues her after the floor underneath her collapses and she falls from the sky, causing the sunlight to damage her face. Eureka calls him an idiot for risking his life to save her but he tells her that he missed her so much and his desire to protect her caused him to do something crazy, and they share an embrace. Due to Renton's strong feelings to save Eureka, the Nirvash evolves into a new form and causes the Fusion Phenomenon. They are able to destroy most of the Azo aliens, even though some of Eureka's skin is damaged from the sunlight. Holland congratulates Renton for retrieving the military's top secret project, which is Eureka, much to the boy's confusion.
The government is revealed to be plotting a mission to destroy the Azo and end its war with humanity. The officials, led by Prime Minister Coda, reveal that the Azo crashed into the Pacific Ocean in the year 2009, and quickly became enemies with the humans, who reacted to it with fear and hate. In order to figure out a way to destroy the Azo, the government and military developed a doomsday weapon that employs solar energy which is called "The Hammer of God". The military also set in motion a plan to build the Megaroad, which is a colony ship that would carry a select 20,000 people to escape from the upcoming deadly winter of ash that would envelop the Earth; however, recent events from the Azo's attacks made it impossible for the military to predict events. They remember the recent loss of lives, which is the Tragedy of Doha that occured 8 years ago; dozens of war orphans were taken into the custody of the military's then Major General Dewey Sorenstam, who turned them into soldiers. Sorenstam was assassinated and the killer was never caught.
However, the military found traces of datu-RA, a drug referred to as growth inhibitors (in other words - immortality) at the crime scene. The governement believes that Sorenstam's then fellow soldier, Holland, had murdered Sorenstam and stole the drugs for himself and his fellow crew members. However, they later learn that Holland is actually one of the original war orphans who was experimented on and is acting as an impersonator of the real one, whom he murdered, and the Gekko crew members, who are the other experimented orphans, had actually assumed false identies.
Aboard the Gekko, Eureka is getting medical treatment while the Gekko crew members decide what their next move should be. In the infirmary, Renton comes to see her and confides in her that he is going to ask for a 2nd lieutenant rank in order to get stationed at anywhere he wants to. He wants to return to Warsaw with Eureka so they can continue watching over the hill. Eureka says that's impossible and confesses that she is not human: she is actually a spy robot created by the Azo to store and gather information on humanity.
This doesn't matter to Renton because he doesn't care about her origins and she was treated no different than him by his parents, and they recall the day they first met: Eureka was in her room when Renton, who had been looking for Nirvash, saw her and told her she was pretty. Eureka goes on to explain that, after she was taken away, she was subjected to horrible experiments by the military and she attempted to kill herself several times but stopped after looking at her necklace. She also learned that, no matter what she or anyone else did, she was going to die soon or later if the red rings in her eyes disappeared due to her short life span.
The Gekko crew members reveal that they need Renton and Eureka in order to reach "Neverland", where they can begin their futures because their lives in the real world had been stolen by the military for conducting experiments on them. The Liberation Army suddenly arrives and the Gekko begins to fight against it. Renton is shocked to find that they are fighting against their allies. Matthiew disables Nirvash and Renton is taken back to the ship while Holland finishes the army off.
Renton is restrained in a dark room as punishment for going into combat without permission. Holland confesses to him that he is not actually a grown military unit leader, but is actually a 17-year-old war orphan, and he and the crew were originally war orphans who were subjected to experiments by the military. However, as the experiment failed, they witnessed a new world that would later be known as Neverland, where they can remain eternally young and begin new lives. Holland asks Renton to join him and the others on their quest to reach that world, but when he refuses and calls them murderers for killing innocent people to achieve their goal, Holland beats the boy.
However he knows that it will be impossible to convince Renton to join them because in order to get to Neverland, they need Eureka, and Renton will never let anything happen to her. Holland decides to use a brainwashing drug on him in order to convince him to join them. Eureka overhears the plot and rushes to get to Renton, who is thrown into the brig.
The army again attacks the Gekko, and with Talho feeling sick a lot lately, Holland is unable to participate in the fight and acts as head pilot for the Gekko. Eureka frees Renton and asks him to escape, but he refuses to leave unless she comes with him. She says she can't go with him because her mission for gathering information on humanity is so that the Azo can learn how to destroy it. She doesn't want that to happen because it will mean Renton will die as well. Renton then vows to fight everyone - the military, the Gekko, and the Azo - in order to protect Eureka.
They launch Nirvash and destroy some of the military units. Renton demands for Holland to answer his question why he wants him and Eureka so badly. Holland explains that he is convinced that Renton and Eureka are part of the legend of Neverland because the Azo planted a crystal inside of Eureka, which contains the password to enter Neverland, which makes her the "chosen girl", and only one person who can open is Renton because he is the "chosen boy".
He then offers Renton a deal: join the Gekko and he will be able to live together with Eureka in Neverland without her ever dying, or taking her away and losing her when she dies. Determined to be with Eureka, Renton accepts the deal and flies away to spend more time alone with her. Then, he confesses to her that he has killed many people and Azo, and wonders why things turned out the way they did. She asks him if they can go somewhere to take a nap together like they did when they were children.
The government learns that Renton's father was the head scientist responsible for the Tragedy of Doha, and both parents are deceased. They search into Renton's background and uncover more of his childhood and military history. During his days in military school, he was frequently abused by classmates for his parents' reputation as scientists. Apparently, the effects of the Tragedy of Doha triggered a black hole over the Earth that lasted for several seconds, and the Azo have the system to read dreams but needed the "chosen boy and girl" to have the same dream in order to achieve this task. This came to be known as the Ageha Myth. They also learn that due to the failed experiment on the Gekko crew members, they are aging three times the normal rate and will die soon.
In other words, they killed Sorenstam and stole the datu-RA drugs in order to maintain their youthful appearances, and are planning to use Renton and Eureka in order to reach Neverland. In order to reach Neverland, the world must be recreated according to the myth, but once "The Hammer of God" is launched, it can not be done. They begin the countdown to launch "The Hammer of God" in hopes it will bring an end to the war for good.
Meanwhile, Renton and Eureka are resting on the Gekko. She asks him if he trusts his crew members, but he says that he is willing to fight them to protect her, which she seems troubled by. Hap and Stoner become suspicious about Eureka being the "sacred maiden" because the book presents her having wings, which she doesn't have. The crystal in Eureka causes the archetypes in all the LFOs to go out of control. Hap and Stoner take advantage of the chaos by attacking her to see if she is a fake. Renton comes upon the assault and beats them, and ends up being shot in the abdomen by Hap. Holland comes in to see what is happening just as Nirvash kills Hap and Stoner.
Renton is hospitalized for his injury, and Eureka feeling that all the recent events are her fault, confesses her love to Renton who is asleep. She then vows to always protect him. The Gekko arrives at Vodarac Shrine in order to meet Anemone (who has a larval form of TheEND), who can grant them access into the other world. Eureka reveals that Anemone is just like her (she is not human and was experimented on by the military) and she was Professor Dominic's fiancée. When they first meet her, she refuses to let them through because their reasons to enter Neverland are not hopeful and they are turning away from reality. Eureka takes Anemone at gunpoint and orders that they get Renton better medical treatment.
Meanwhile, Renton wakes up to find the spirit of the professor by his side. He apologizes for his failure to protect Eureka, but the professor tells him not to let go of his feelings, and to focus more on what's in his heart than in his head. With that, Renton rises up and launches the Nirvash just as the Azo attacks the group. Anemone is able to stop time briefly and tells Eureka that Dominic had halted the experiments when he saw the results. Anemone proceeds to tell Eureka that the Azo are intelligent living creatures that are unaware of their origins and merged with the planet as part of their nature.
However, due to that she and Eureka were created by the Azo, if they die, so will the planet. In her horror, Eureka asks what should she do to stop that, and Anemone tells her that she needs to have a dream that will come true. In the newly evolved Nirvash, Renton then destroys the Azo alien, and asks Eureka to leave with him because he loves her with all his heart. She agrees without hesitation. Realizing that letting Renton and Eureka leave will mean the end of his dream, Holland angrily vows to never let them escape.
Renton and Eureka confess their love to each other and decide they want a future together. Although they are unsure of where they should go, all that matters is that they are together and happy. Their moment is cut short when they are attacked by Holland, who is determined to see that the future of him and his fellow crew members is fulfilled. Renton shouts that he is so wrapped into his past with Eureka that he actually can't stand it, therefore he is not going to reconsider returning to the Gekko and help them get to Neverland.
The battle is intense, especially due to Renton struggling to remain awake after losing too much blood. To kill the couple, Holland activated the Devilfish's ability to see "souls" to finish the battle off. However, it only led him to discover that Talho is pregnant with his child, and with that he abruptly stops the battle, having lost the will to fight. He later learns that the baby is not affected by their aging acceleration, and is their hope of a new future, which brings an end to their goal for good. Renton however loses consciousness due to blood loss, and Eureka desperate to save him from dying, decides to sacrifice her memories to save him.
She tells him that although she has learned how hateful the world truly is, she wants to save it because it is the planet that she met Renton on. Although saddened about him forgetting about her, Eureka says that her ultimate dream is for him to always remember her and their relationship in dreams, and with that she will live on beside him, and she loves him more than anything. The Nirvash then pierced the Command Center so that "The Hammer of God" can enter the Command Center to destroy it and the Azo for good. As a result of the Azo Command Center being breached, the Second Great Flood occurs and millions of people perish, but the Azo is destroyed.
The survivors on the planet witness the defeat of the Azo and the transformation of the planet as it returns to normal for the first time in 45 years. Coda arrives at the Vodarac Shrine to witness the planet's changes and meets with Anemone. Having witnessed Dominic's dream of ending the war come true, Anemone disappears with the Azo and is reunited with Dominic in spirit. Meanwhile, the Gekko crew, having crashed landed due to the Gekko malfunctioning from the chaos, observes the changes on the planet and contemplate their new futures.
When Renton wakes up, he finds himself on the coastline of Warsaw and sees a naked Eureka with long hair and incapable of speech. His gunshot wound is also gone and Larva Nirvash is huge in size. Renton realizes that Eureka had sacrificed her memories in order to save him and stop the Azo, but in the process, she turned into a full human (noted by the absence of the red rings in her eyes) rather than disappear with the rest of the Azo, likely due to the Azo granting her dream of saving Renton after willing to sacrifice her memories in exchange for saving his life.
Larva Nirvash bids farewell to Renton and tells him that he and Eureka can fly even without wings, and that their own two feet can carry them to the future, before it disappears into fragments of light. Although Renton is saddened by Nirvash's departure, he finds solace that Eureka is still with him, even if she has changed. As Renton and Eureka (who is wearing his jacket) wonder around the coastline, they look up the sky and see two rainbows and a rescue shuttle to pick them up. Eureka kisses Renton on the cheek and they hold hands. Renton realizes that the professor and Nirvash were right about their dreams coming true and he smiles as he knows that he and Eureka will have a happy future together.
- Yuko Sanpei as Renton Thurston (Young & Older)
- Kaori Nazuka as Eureka (Young & Older)
- Sakiko Tamagawa as Nirvash & Diane
- Shigenori Yamazaki as Dominic
- Ami Koshimizu as Young Anemone
- Keiji Fujiwara as Holland
- Michiko Neya as Talho
- Tamio Ohki as Ken-Goh & Kuzemi Swigert
- Taro Yamaguchi as Hap
- Tetsuo Komura as Jurgens
- Tomoyuki Shimura as Jobs
- Yasunori Matsumoto as Stoner
- Yoko Soumi as Mischa
- Akio Nakamura as Matthieu
- Cho as Woz
- Fumie Mizusawa as Gidget
- Kenichi Ono as Morita
- Mamoru Miyano as Moondoggie
- Mayumi Asano as Hilda
- Sachiko Kojima as Maria
- Mariko Akashi as Coda Lovell
- Mugihito as Braya Mattingly
- Sakiko Tamagawa as The End
- Takeshi Aono as School Principal
- Yoshiko Sakakibara as Old Anemone
- Yuriko Yamaguchi as Female Engineer
- Takeshi Aono as Axel
- Michiko Neya as Maurice
- Eriko Kigawa as Maeter
- Fumie Mizusawa as Linck
- Johnny Yong Bosch as Renton (Older)
- Stephanie Sheh as Eureka (Young & Older)
- Melissa Fahn as Nirvash & The End
- Peter Do as Dominic
- Kari Wahlgren as Anemone (Young & Old)
- Crispin Freeman as Holland
- Kate Higgins as Talho & Linck
- Kyle Hebert as Ken-Goh
- Tony Oliver as Hap
- Michael McConnohie as Jurgens
- Dave Mallow as Jobs
- Doug Stone as Stoner
- Mary Elizabeth McGlynn as Mischa & Maurice
- Kirk Thornton as Matthieu
- Dave Wittenberg as Woz
- Jessica Straus as Gidget
- Terrence Stone as Morita
- Steve Staley as Moondoggie
- Megan Hollingshead as Hilda
- Peggy O'Neal as Diane, Maria & Maeter
- Barbara Goodson as Coda Lovell
- Michael Forest as Braya Mattingly
- Steve Kramer as School Principal
- William Frederick Knight as Kuzemi Swigert
- Julie Ann Taylor as Young Renton
- Steve Kramer as Axel
- The main song for the film is "Space Rock", by iLL.
- The Yuhoo website reporting Dominic's death, Morita giving Koda a printed Ageha Mythology from a website called Ryukipedia, and the big red circle icon seen by Koda on the video screen at Tresor about Renton's past is a reference to the real-life Yahoo, Wikipedia, and YouTube websites respectively.
- The Gekko being part of The People's Liberation Army Mobile Forces is a reference to the real life army called People's Liberation Army or PLA, which is a unified military organization of all land, sea, and air forces of the People's Republic of China.
- The number on the Independent Youth Unit "303" is a reference to Holland's personal LFO Devilfish Type303.
- Holland's ability to sense souls within a living being upon activating his Compac Feedback System is never evident in the TV series. This ability bears a striking resemblance to the character Maka from Soul Eater, one of BONES' previous anime works.
- Eureka's last name is Zita, which is a reference to the word "Zeta". In the system of Greek numerals, it has a value of 7. Eureka never had a last name in the TV series until the final episode when she marries Renton and becomes "Eureka Thurston".
- Renton and Eureka are discovered to be the chosen children to pass through Neverland due to their ability to have the same dreams. In episode 11 of the series, Eureka said to Renton that she cannot dream.
- The term Doha in the Tragedy of Doha is used by fans of the Japanese national football team to refer to the qualification match for their 1994 FIFA World Cup match with Iraq, held in Doha, Qatar on October 28, 1993. The Gekko crew played soccer in episode 39 of the series.
- Holland and Talho's younger selves closely resemble Norb and Sakuya from the TV series.
- Renton's birthday is December 8, 2040 (as according to his military background form) in the film, whereas it was February 28, 11990 in the TV series.
- The Gekkostate crew, Dr. Bear, Diane, Axel, along with Eureka and Renton's 3 adopted kids play different roles in the film compared to the series. In the film, the crew were war orphans who were experimented on by the military and took on fake identities; Dr. Bear was a famous military leader who was actually Holland Novak and murdered by the orphan who took his identity; Diane was a scientist who offered Koda information about the Ageha Myth; Axel was the principal of Renton's military school; Whereas Maurice, Maeter and Linck were presumably foster grandchildren of Axel's. In the TV series the Gekkostate was military fighter including that Dr. Bear is a member of the Gekkostate. Diane is Renton's older sister, while Axel is Renton's grandfather whereas Maurice, Maeter and Linck are Eureka's adopted children.
- Dewey was named "Dewey Sorenstam" and was the military leader in charge of the experiments on the war orphans, and was murdered by the orphan who took on the identity of Holland.
- The ship captain who pressed the button for the Hammer of God to activate was one of the Sages from the series, instead of Dewey.
- The Hammer of God weapon is similar to the Oratorio #8, which Dewey used in the series to destroy the Scub Command Cluster.
- Eureka's undergarments worn by her when she is looking at herself in the mirror resembles those worn by Talho in the TV series prior to episode 30.
- Eureka's green skin upon exposure to sunlight bears a resemblance to her condition at the end of episode 43 due to her being in close proximity to the Command Cluster. Unlike the TV series, her green skin heals itself.
- Eureka never killed people in the film, while only Renton does to the point where he will kill those who prevent him from being with Eureka forever. Whereas in the TV series, Eureka and Renton did kill people which made them become horrify at what they done. Due to this, they both become pacifists by removing the robot fuel from the UFOs so the victims won't fight, and so they don't get kill.
- Anemone's blank book is a reference to the TV series, whereby humanoid Coralians' individual books are blank and are written based on their experiences with the humans.
- The Seven Swell is seen in the film but no one knew what is was and people described it as a "joyous song" by the planet.
- The syringe that the Gekkostate uses to inject themselves with contains a drug that delays their aging acceleration, which bears a resemblance to the syringe that Anemone uses in the TV series to harden her mental state so she can pilot theEND.
- Dominic's fate is similar to that of Adroc Thurston, Renton's father, in the TV series. However, in the film, Dominic actually perished in a military experiment while Adroc disappeared and his mental state was transferred to the Command Cluster.
- Eureka and Anemone were born as spy robots from the Azo in the film, which is similar to Eureka being born as a humanoid Coralian by the Scub Coral to observe humans but Anemone is an artificial humanoid Coralian in the TV series.
- Dominic is a military scientist specializing in human experiments in the film, whereas he is a second lieutenant in the military and his first and only experience in human experimentation made him physically sick in the TV series.
- In an uncredited scene, Charles and Ray were Renton's parents and the leading scientists in the Tragedy of Doha. Whereas in the TV series, Adroc is Renton's father while Axel only mentioned Renton's late mother in episode 1.
- The girl character in Ageha Myth book that Hap and Stoner read is a reference to what happened to Eureka at the end of the TV series; having wings, having a soul mate, and ending a war without fighting.
- Neverland, Peter Pan, and Wendy are mentioned in the film.
- The final scene of the TV series' ending with circle of trapar around Earth and Renton and Eureka's names craved into the moon is shown in the film upside down from when Holland recounted his past to Renton.
- Larva Nirvash and Larva theEND are at odds with each other, a reference to them fighting in the series.
- In the final scene in the film, Eureka's big smile to Renton is a tribute to her first smile in episode 1 and her wearing his jacket is a tribute to how she wore his tracksuit in episode 24.
- Eureka's sunlight phobia is a reference to a chapter in the Golden Bough called "Between Heaven and Earth" and in it a sub chapter called "Not to See the Sun", whereby those who were to be rulers or commanders, whether men or women, were to be locked up for several years when they were children, some of them 7 years, and this so close that they were not to see the sun for if they should happen to see it, they forfeited their lordship.
- The ending catastrophe in the film is a reference to Noah's Ark.
- Renton and Eureka's hometown is Warsaw, which was a ruined city in the TV series.
- The Azo is also called the Image, whose behavior is similar to the god in Noah's Ark, whereby God is observing the Earth's corruption and deciding to destroy all life. However, God found one good man, Noah (Renton), a "righteous man, blameless among the people of his time" and decided that he would save him. God instructed (Ageha Myth) Noah to make an ark for his familu and pairs of the world's animals. In order to remember the promise with Noah for offering sacrifices to him, God put a rainbow in the clouds, saying 'whenever I bring clouds over the earth and the rainbow appears in the clouds, I will see it and remember the everlasting covenant between God and all living creatures of every kind on the earth".
- Anemone's mentioning of Image being a mirror is a reference to the story of "Through the Looking-Glass, and What Alice Found There (1871) by Lewis Carroll.
- Eureka's long hair symbolizes her gaining freedom from the Image and being able to live happily with Renton, as cultural history of having long hair, "having long hair signifies being outside of the system of society" In Jewish and other cultures, long hair signifies mourning or sadness.
- The 1246 seconds of the Hammer of God's activation time is a reference to the duration of the Antibodies active period in the TV series.
- Gonzy never appeared in the film, whereas he was a humanoid Coralian observer on the Gekko. His role as an observer was passed to Anemone in the film.
- The famous motto of the TV series "Don't ask for it. Go for it. In doing so, you shall be rewarded" is mentioned once by Dominic when Renton sees his spirit in the sickbay.
- The number of crystal flower seeds on Renton's bracelet is 4 while Eureka's is 3. Add them together and that makes 7.
- According to a Japanese interview with the Japanese voice actor of Holland and the director, Tomoki Kyoda. The name for Holland and Talho's child was intended to be "Mirai", which means future in Japanese and is feminine, strongly implying that their child was indeed a girl. But this could be strictly meant for the film, due to that the name and gender of their child were never revealed in the TV series.
- Renton and Eureka never kissed on the lips in the film, although Renton attempted to prior to him being shot by Hap and Eureka kissed him on the cheek in the ending, which breaks the tradition of the TV and manga versions.
- Renton rescuing Eureka from the Image and fleeing away to find someplace where they can be together, reflects what Renton thought in episode 30 about running away with Eureka to somewhere to avoid the war.
- Eureka's name is never displayed on the Compac Drive.
- Renton understands what Nirvash is saying in the film, whereas it was Eureka in the TV series.
- Renton and Eureka were childhood friends and fell in love at first sight at the age of 6 in the film, whereas they met at the age of 14 and it was love at first sight for Renton, but unreciprocated for Eureka in the TV series.
- It was Renton in the Nirvash when he and Eureka reunited at 14 in the film, whereas it was Eureka in the Nirvash when she and Renton first met in the TV series.
- The only time Renton was afraid to lost Eureka was when he saw get taking away by military soldiers during their childhood. He also feel guilty that he couldn't do anything to save her during that time. This incident made them be separate for eight years. Whereas in the TV series, Renton was scare to lost Eureka after she get absorb by the Scrub coral that was inside a tree. Due to Eureka being in a weird condition, Renton blames himself for not getting there in time to save her even though he didn't know how she got that way. He also becomes afraid when Holland physically abuses him and this incident made Renton not being able to see Eureka in her hospital room. Therefore Renton runs away while thinking that everyone in the Gekkostate hates him for what happened to Eureka.
- Eureka faints in Renton's arm during his first battle against the Azo in the film, whereas she faints several times in his arms in the beginning of the TV series.
- Renton tells Holland that he and Eureka are going on a date and she freaks out in embarrassment in the film, whereas they never went on a date in the TV series.
- Eureka feels guilty when Renton gets shot by Hap after she was attacked in the film, whereas Renton felt guilty for Eureka nearly being absorbed by the Scub Coral in episode 19.
- Although he serves with the military, Renton is never seen holding a gun and Eureka threatned to shoot Anemone with a gun in the film, whereas Renton and Eureka have used guns but Renton never discharged one in the TV series.
- Eureka pressuring Holland to take Renton to a hospital for his gunshot wound in the film is similar to how Renton asked for Holland to take her to a hospital for the scubs on her body in episode 20. In both versions, the requests were rejected.
- Renton apologizing to Eureka that he won't be able to keep his promise of them being together due to losing lots of blood from his gunshot wound in the film is similar to how Eureka apologized to Renton that she wont be able to keep her promise of them being together due to her becoming the new Command Cluster in episode 49.
- Eureka leads Nirvash to penetrate the Azo Core in the film, which is similar to how Renton flew Nirvash into the Command Cluster in episode 50.
- Eureka was rescued by Renton first after reuniting in the film, whereas it was Renton who was saved by Eureka after they first met in episode 2.
- Renton is the pilot of the Nirvash in the film, while it was Eureka who was Nirvash's pilot (although she temporarily gave that role to Renton half-way through the series) in the TV series.
- Eureka was cared for by Renton's parents (implied to be Charles and Ray) during her childhood in the film, which is similar to how Eureka was cared for by Adroc (Renton's father) but she retained the appearance of a 14-year-old girl in the TV series.
all information on the Eureka Seven movie came from http://eurekaseven.wikia.com/wiki/Eureka_Seven:_Pocketful_of_Rainbows