Germany, 1970. Gherta's visit to a museum dedicated to Conrad Rontgen affects her profoundly. Years later, she is confronted by Duma, who entrusts her with important research into the Fragments and some kind of machine. Duma himself appears to be acting on behalf of other, more insidious forces. Meanwhile, back in the main plot, Helga remembers lots of things about her past life as Seraphine.

Christina was a teacher in Spain in the 1700s. One of her students died tragically for her sake. Princess Tina of Girishia meets the half-human, half-machine Soran when she gets lost in the woods as a young girl. Fast forward some years, and Tina is nearly 16, and preparing to get married to Sesu, another young noble, until she falls in love with Soran instead. Meanwhile, her uncle, Georca, is plotting to overthrow the king, and the Children begin their fateful work on reincarnation.

The Girishian scientists meet with the King to discuss a new form of energy for powering their civilisation via the Zone, but tragedy strikes when a terrorist attack on the King accidentally involves Tina. In a last ditch effort to save her life, they use OSL to revive her. The experiment is a success, but the King chooses to use the power of OSL to turn Tina into a living weapon. This news filters back to Georca, who then kidnaps Hiisuma in order to control her. Meanwhile, Tina goes to visit her estranged mother, but Georca has more machinations in store...

Dumas reveals the fate of the Children once they return to Girishia, but makes a bargain with Hiisuma over a solution to the problem whilst abusing his knowledge of Gherta. Armed with Hiisuma's information, Dumas attacks the Children and captures Helga. While Thoma has a bizarre reaction to Helga's revelations about her past lives, Agi and Soreto give chase to Gherta's old laboratories, where they face Enma once more and meet some familiar faces...

Thoma and co give chase after Dumas to Kuril Island, where he reveals the tragedy of his past to Helga before taking her to Georca, who sets the final preparations for his return to Girishia in motion. Meanwhile, Gherta finally decides to confront her fears about Dumas' knowledge of her past, while Cooks and Alice resolve their search for the Children before beginning to deal with the GED Organisation and the mysterious stone once and for all.

Dumas sends out his robot minions to take control of the GED Ring and the Organisation itself, while Cooks sneaks in to to stop its activation. Meanwhile, Dumas himself detaches the segment of Georca's ship containing the bodies of the Girishian scientists and sends it crashing to the ocean - while Hasumodai, Talrant, Chitto and Thoma escape unharmed, and the bodies are left unscathed, Hiisuma's despair at Dumas' betrayal leaves him catatonic so he doesn't escape properly, and he dies on a beach with the other Children looking on sadly. In the meantime, Agi and Soreto confront Gherta with the truth about her past - that she was once Mel - and we learn why she lost her memory so suddenly in the first episode, as well as some more information about the Fragments of the Autozones.

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Dumas starts the final phase of transferring Helga's soul, but not without a fight as Gherta turns on him with some help from Cooks - however, Dumas is well prepared for any eventuality. A last minute change of heart and a moment of defiance are almost met with tragedy, however, and Helga's last hope lies with Thoma as he journeys into the Zone to save her soul.

Helga pursues Thomas into the dark zone. As the two meet, Thomas reverts to Sessile, and reveals all. His heart still burdened by the death of Seth, Sessile decides to sacrifice himself. Tina follows him, trying to dissuade him, for not only he, but Thomas as well will go. In the end, Tina appears and comforts Sessile. With sessile and Tina put to rest, Thomas and Helga return to earth. On earth Duma plans to take his fathers body and the ship and return to space, where he plans to place himself in a state of suspended animation alongside Tina's statue. As for the Be forte children, they decide to live their newest incarnations to the fullest. Helga hangs clothes outside an orphanage, and a traveler comes in for a glass of water, on his arm is a scar that resembles a Grecian name.

Dumas and Thoma fight for Helga, but Dumas has the upper hand thanks to being superhuman. Undeterred, Thoma and co. head off to find Helga once more, but Thoma is strangely entranced when he discovers Tina's body in one of those giant cylinders. The sight of it brings back Thoma's repressed memories... Dumas finally defies Georca for once, and after being beaten Helga attempts to stand up for him to no avail. Finally they bond as brother and sister, and Helga beseeches him not to go through with his plan to kill Georca - however, Dumas knocks Helga out, and as Thoma is wracked with guilt over his past transgressions Dumas teleports outside the ship to finish his machinations...

Helga and Thoma are pursuing Chit into the forest. They find him unconscious and covered in killer bees. Thoma is apiphobic, and hides in a bush grimacing while Helga has to calmly rescue Chit. Thoma and Chit then run into Talrant, one of the Children, who is still trying to trace the next incarnation of Christina and is attacked by a shadowy creature again. Thoma spars with him for a while and almost has the upper hand, but Talrant breaks out a big shiny robot called Wanda to do his bidding and scare off Thoma. Meanwhile Cooks and Alice do more investigation into GED, and the Children re-iterate their frustration over their inability to find Christina.

The GED Organisation prepares for the activation of the Ring, while the Girishian spaceship readies to leave Earth as Thoma continues to penetrate deeper within to find Helga. Hasumodai and Talrant are confronted with major setbacks in their quest as Dumas reveals the extent of his machinations, while Agi and Soreto confront Gherta as the pieces of her past begin to slot together.

The Children and the Intrepid Trio head back to Kokkuri, where the Children use a special machine to determine that Helga is indeed the reincarnation of Tina. They then actually reveal some details about what the heck is going on after all this time...

Helga and Chit are caught up in a storm and rescued by a ship which turns out to belong to the GED Organisation - Gherta is on board attempting to trace Kirchner, who appears to still be "alive". Meanwhile, the Children track Helga to Kokkuri Island at about the same time as Thoma goes searching for her, and they decide to stick together in order to find her - however, they are unaware that Kirchner is coming closer to the research ship, and Shiberu is also on board.

Thoma brings Chito and Helga to his secret island, Kokkuri, where he's made provision for hiding out. When Chito runs off into the forests to get fruits for her, Helga is completely absorbed in her painting and fails to notice. Thoma ends up running into the forest after him with Helga following behind despite Thoma's repeated insistence that she'll just get in the way. Meanwhile, on the mainland, Cooks continues to investigate the Children. The old man from the end of the last episode is brought to the police station but dies soon after, and is identified as a man named Glass who went missing several years ago. Video footage of him in custody shows his dead mother sitting beside him until she suddenly vanishes.

Cooks and Hollingworth travel to Clairmont and listen to Cooks' recording of the diary of a scientist named Radcliffe. Cooks' grandfather witnessed the death of Befort's Children in 1901, discovering a strange black stone at the scene. On handing this to Radcliffe, he begins to investigate it with the aid of X-rays and discovers numerous indecipherable, constantly shifting inscriptions inside. The GED Project was then set up to investigate the stone, but Radcliffe eventually discovers that the British government was already aware of Befort's Children and so journeys around Europe chasing their pasts. We discover that the children are named after a small village in Belgium, where the earliest record of their existence (1489) was found. However, Radcliffe was driven mad by his obsession with the Children and eventually was discredited and died.

Cooks and Alice investigate Gherta's home and old laboratory, discovering her bedroom is entirely devoted to Conrad Rugen. After some more snooping around, they find their way into the GED research labs, where not only do they find evidence of their involvement with the aged scientists but of investigation into the Fragment scriptures. Meanwhile, Gherta faces the board of directors of the GED Organisation, attempting to stall over future OSL experiments despite her hypotheses about the Fragment - however, when the man funding her experiments makes his appearance, it appears that the GED Organisation is really not who she needs to be wary of.

Georca reveals all to Tina, whose anger leads her to open the Zone and transform into a living weapon. While she does lay waste to much of Girishia, the day is unsurprisingly saved, but not without cost and sadness for many.

The Children visit Sweden in 1901, where Palza/Conrad is being awarded the Nobel prize for discovering X rays. Flash forward to 2012, and while Helga is incarcerated in Chikao, the Children investigate more into Serafine's paintings, but are attcked by mysterious shadow creatures. The Children part ways once again - some to find someone who they believe to be the reincarnation of Serafine, others to try and find Mel and Palza to deliver their memories to them. Helga and Chit escape from Chikao once more, while Thoma has srange nightmares and can't shake Helga from his mind. The Children, Helga and Chit all board the same train bound for the mainland, and Thoma is left with doubts in his mind...

A policeman, Cooks, visits a family where one of the Children used to live, in an attempt to find out what's going on. Helga and Chit are recaptured on the mainland and sent back to Chikao, which please neither of them - especially since Chit is getting sent to another orphanage. A crazed speedboat driver (the man from the first episode with the cryptic ramblings) crashes into the boat carrying Chit, however, and Thoma happens to be on hand to rescue him, so they set out together to rescue Helga once more.

The discovery of Helga's whereabouts bring only brief cheer to the Children, as a strange explosion occurs nearby - Cooks and Hollingsworth investigate to discover a man named Kirchner abducted his younger sister from a house and made it explode with some kind of strange blue energy - Kirchner has undergone the same process as Shinon, and the Children explain it as something to do with "OSL", which emanates from the "Zone". The Children confront him, but before they can do anything for him he is shot by Phantom GED forces under Duma's jurisdiction - his OSL lashes out unpredictably, and he disappears like Shinon and Grass did before.

Chit and Thoma head back to Chikao to rescue Helga, but have to take extra care since there seems to be policemen searching the island for escaped prisoners. They succeed in breaking her out, but Helga is totally reticent towards Thoma despite how he repeatedly saves her life. As they escape through the forest they come across one of the prisoners, Shinon, who is in no way what she seems - and Helga has disturbing visions associated with her that Thoma and Chit cannot see. The "policemen" advise them to forget about Shinon, and they escape from Chikao once again - meanwhile, one of the other "prisoners" has found their way elsewhere...

A man sits alone in his study surrounded by scrawlings and mumbling about a forthcoming apocalypse as we see a photo of a group of ageless young albinos called the Befort Children. We switch focus several times as we follow the Children throughout history - in Holland, where their attempts to convince a young boy called Conrad to join them fail after they send him a postcard depicting a strange image, to Sweden at the turn of the century, and to the South Eastern Islands where they arrive too late at the bedside of a dead woman named Serafine who has been painting the same image as on the postcard. Strangely, one of the Children, Mel suffers amnesia and panics, getting captured by the strange young man Duma and his cronies while the other Children escape. Fast-forward to 2012 in the Islands, and the roguish Toma practices his martial arts before discovering a young girl, Helga, lying on a statue silently.

Kirchner starts to lay waste to the research ship in his attempts to reach Shiberu, but is attacked by the mysterious black entities that are after the Children, and we finally learn something about them. Agi's attempts to calm Kirchner and stop them is in vain, however, and the whole affair ends tragically. Yet now the Children and Helga are reunited, they decide to explain everything - particularly where they come from.

Georca takes advantage of the confusion to attack the palace. The Children try to save Tina, but discover that there are complications leading to only one real solution - transfer her soul to Earth. Yet tragedy strikes once more... Back to the present. While Helga deals with the sudden flood of new memories, Hiisuma gets himself into confrontation with Duma, Cooks plots to stop GED, and Thoma is left unsure what to do next.