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Jouju-in Cemetery is a place of sacred burial in Kamakura, adjacent to Jouju-in Temple, located within sight of the sea, and near to both Yuigahama Beach and Gokurakuji Train Station. Within the Elfen Lied universe, it is the sight of a major and brutal confrontation, as well as being in the background of many scenes in both versions of the series.

Established in the 13th Century, the cemetery is, like much of Kamakura, marked off by the period of the Shogunate in that region. Its headstones are large and ornate, and its grounds scenic and haunting, its structure multi-leveled and striking.

The first time it is seen in full during the series is when Nana makes contact with Lucy, demanding she return to the Diclonius Research Institute, a demand Lucy naturally refuses, offering instead to let Nana leave without incident. When Nana refuses and instead asserts that she will take Lucy back by force, the battle between them begins with Lucy knocking Nana back against the nearby stone stairwell's sides. Nana counter-attacks and for a time holds her own, and their attacks begin to damage the headstones and other grave markers. At a critical moment, Nana is distracted by the presence of Mayu, an opening Lucy uses to begin dismembering Nana. Nana almost bleeds out on the pathway through the cemetery, and is only saved from being finished off by Lucy by the presence of soldiers led by Nana's 'Papa', Kurama, with a sniper shot only just missing Lucy. Nana, despite her vast agony, manages to use a special ability and disables Lucy's vectors, inspired in part by the peril to her 'Papa'. Struck by a despondent Kurama, surrounded by soldiers and unable to retaliate, Lucy flees, confusing her enemies who take away the gravely wounded Nana. Presumably, some aspect of Kurama's authority to keep matters concerning Diclonius a secret came into play as to the damage done to the cemetery or any possible witnesses beyond Mayu, who was knocked clear and therefore not known of. At least in-story, no one else seems to have witnessed or noticed the battle. Like many Kamakura sites seen in the series, the cemetery's depiction as being completely empty of people is not consistent with real life.

This image of a largely unattended site persists in its next prominent appearance, wherein Nana returns to the cemetery after leaving the Diclonius Research Institute, unsure of how to proceed in the world, staying inside an undefined structure that may be a shrine, mausoleum or maintenance shed. On the one hand, it can be seen as odd that she would go back to a place where she had seen so much pain. On the other hand, this spot was one she knew, and lacking social skills or knowledge of the world, any familiar spot might be a comfort. Since she saw the island facility as a home despite the pain she knew there, perhaps a place otherwise uncomfortable might seem more acceptable to Nana. In any event, she lacks knowledge of money in order to support herself, resorting to not only burning the money Kurama gave her as fuel, but using pieces of fencing scrawled with prayers for the dead, unconsciously vandalizing the centuries-old site. She is corrected on this by the arrival of Mayu and Wanta. Mayu is at first stunned that a girl she saw lose her leg (that is all Mayu saw before being brushed aside by Lucy) seems now intact, and attempts to dismiss her memories of this as muddled. After testing the horned girl's knowledge (or lack thereof) of how the world works, Mayu offers to take her back to Maple House, where Nana is especially intrigued by talk of another girl like her, thinking (correctly) that she may be Lucy. After her confrontation with Nyu, the series differs on where a tearful Nana flees to; the manga has her flee to a gazebo-like shelter in the forest that seemingly does not exist in the real world; the anime has her flee to the venerable Michibiki Jizoudou shrine.

These are merely the two most prominent appearances of this ancient cemetery. It is often seen in passing or in the background, especially as the characters use the frequented stone stairwell that at times seems to have Maple House at its center.

Whether the cemetery is the resting place of any known characters in-series is in question. Chief Kakuzawa seemed, for reasons of tradition and secrecy, to insist on all members of his family being buried in the grotto beneath the island facility, and it is here he met his end. Indeed, this dim, dingy, oppressive and even toxic site can be seen as a dark echo of picturesque Jouju-in, which would have been founded near the time when the Kakuzawas' ancestors were hunted and forced to flee to the island which would one day house the Institute.

Kouta's sister Kanae and their father, for example, could have already had burial arrangements nearer to their home in Hokkaido. In real life, it would require that either Kouta's and Kanae's father, their mother (fate unknown) or one of Yuka's parents belong to the Buddhist sect that oversees the cemetery.

In the manga finale, a grave site for Mariko Kurama is seen, attended by Nana and Kurama, though whether this is at Jouju-in cannot be determined from the imagery of those pages. The cemetery is almost certainly nearby in the anime finale as Kouta and Lucy meet for the last time onscreen, and share their only kiss.

Of Jouju-In Cemetery in the series, whatever the version, it can be said that neither the living nor the dead know an entirely quiet time.

Thanks as always to User Yoshik for information vital to this article.