Magna Carta has about a dozen huge plot twists during the course of the game. By the time I reached the end, I realized the manual was filled with lies and surface descriptions to intentionally throw players off guard. Keep in mind even this is not the truth, but an interpretation of the events that happened in the story.
Juclecia's true story starts with Estell, her mother. While known as the second wife to Clive Reopold Re Ecritian, she secretly worked as a spy for Vermilion. Estell still had a good heart and her involvement with the terrorist group was done in good intentions for her home country. Estell even became an adoptive mother-figure to a lost boy named Tristan.
Tristan got separated from his parents when the Kingdom of Krois was destroyed by Clive. His mother (Ladrinne Morei Rune Sirat) escaped back to Sirat thinking her husband and child died, and it's unknown what happened to his father. Tristan somehow ended up in the garden at Ecritian Palace and met Estell, who reveals her true, loveable tomboy personality when with him. For a short and peaceful time, Juclecia and Tristan played with Estell in the old garden. This got Tristan out of the long depression of loosing his family and home.
One day during a private meeting at the Holy Land (in the destroyed Krois Kingdom) Estell was murdered by the leader of Vermilion, Unbeter. Unbeter of Krois had growing suspicions of her and believed she had breached his trust. Tristan was hiding and saw what happened. Horrified, he came out of hiding and called Estell's name, and unfortunately Unbeter noticed him. Tristan couldn't forgive Unbeter, and using a short sword he stabbed at the surprised Unbeter. As Unbeter died, he realized it was his own son, Tristan. Tristan began to remember the man's face, and became irreversibly shocked because he had just murdered his own father.
Unbeter's memory was then transferred into an object he had (known as an Emblem, an Emblem takes many forms, and in the game you see it as Calintz' necklace), which then transferred into Tristan. Young Tristan's persona became foggy, in the confusion he ran away from the scene, and then fainted. Helios Ryuad Rune Sirat (Tristan's real grandfather on his mother's side) who witnessed the incident took him under his wing, and raised him as his own son. Helios had a liking towards Tristan's amazing sword skills and wanted him to succeed him as King of Sirat. Helios also had Tristan renamed to Calintz.
This Calintz has memories of a happy childhood with a woman called Estell, and he believes a man named Tristan killed his father and Estell. He also does not know who his real mother is. Ladrinne, who would normally succeed the throne also does not like the idea of someone else succeeding (she also doesn't know who Calintz really is).
Soon after news of Estell's death had spread, young Juclecia was exiled from Shudelmir Kingdom, and died. Willight Riziem Ernst, a man seeking ways to gain power quickly and who knew about Juclecia decided to bring her back to life, in a way. He made a fake Imperial Princess using his own Emblem and the body of a girl, Adora. Using this power, Willight erased Adora's memories and then transferred Juclecia's memories and appearance into Adora. He then raised and educated her in the ways of politics and arts, recreating the real Juclecia.
However the original Adora still exists, just barely. Every now and then Juclecia actually reverts to Adora, and back again. During the game Juclecia makes her return to Shudelmir, as does Calintz. Calintz is ordered by Helios to escort Juclecia safely, and after much confusion (Rose impersonating Juclecia under Tristan's orders to have her killed and infiltrate Shudelmir) she arrives. From there the story goes on, Juclecia meeting Leona, Shurenlord and the rest of the story's key characters. Every now and then Adora appears and suspicions of her and Juclecia being false arise.
Willight's plan seems to come together, but Gilbert Ropponso Descralda who also is aware of Emblems and their power (since he too has been seeking power since Unbeter's death, he really is Jade and used one to become Gilbert) finds out. He finds Willight's Emblem and destroys it, which also destroys (the unreal) Juclecia forever. This leaves Adora lost and trying to find out who she truly is.
Also, the Emblem sometimes has a mind of its own. When Adora first met Calintz in the garden she received Estell's memory from Calintz' Emblem. She also instantly befriends Calintz in the same bittersweet way Estell did with young Tristan. When she first meets him, she even tries to get Calintz to "remember her". Adora isn't only driven by Estell's memories, but she really loves Calintz in a different way. When real Adora starts to come back, and during her search for self identity, she and Calintz fall in love. Calintz also always notices that she resembles Estell, which makes him love her even more.
The Emblem's effect on Calintz slowly makes his real personality and appearance change permanently into the evil persona created inside him, Tristan. This is the same Tristan in Vermilion who has been working against the party throughout the whole game. In the end, the party fights Tristan and Adora destroys The Emblem to save Calintz' real persona. However, she also knows that by doing this, she disappears forever..
The ending theme song really sums up the theme of the game, and carries the sad feeling of the entities Estell, Juclecia and especially Adora combined.