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Eventually, Leymore learns that Cai "betrayed" him by allying himself with Fomorians. However, Leymore had forgiven his best friend and tries to locate him, but to no avail.
He learned Alchemy when he was a young boy, and used it to impress Jenna and then took care of her. She wants to help Leymore, but he thinks it's something too dangerous for her to handle. Eventually, the Templar Knights asked her asked to kill Leymore, but turned down that offer and resigned.
Leymore, along with Jenna, partakes in the final battle during Claimh Solas's resurrection. With help from the Milletian, they overpower Tethra, who informs them that they are too late as he dies. Leymore and Jenna urge the Milletian to rush on while they hold off the remaining Fomorians.
As the Milletian battles against Claimh Solas, Leymore encounters Cai. The two of them destroy the rooftop barricading the Milletian and Claimh Solas, allowing them to call Adniel for help.
After Claimh Solas is defeated, it attempts to 'self-destruct'. Leymore stops this event, at the cost of his own life. Cai then sacrifices himself by resurrecting his fallen comrade.
Leymore visits the site where Cai sacrificed his life and reminiscences about it. He then places a flower and heads for Shadow Abb Neagh, searching for Elatha. He heard about Elatha from Andras. Leymore hopes to find answers regarding Cai's death, as it is unnatural cause. Eltha responses that even a "Noitar Arat Alchemist" was ultimately human in the end. Elatha also finds it sad that Humans waste their time seeking comfort for their grief, regarding it as a "sad fate." Elatha then asks Leymore if he understands that fate is the greatest of privileges given to humans. He then remarks that it is not the same as the tedious eternity Gods must endure. Elatha explains that a Shadow Walker is forced to spend an eternity suffering, a pain greater than facing death. He then says that it is now the penalty Cai faces for using the Alchemy of Caliburn to bring a life back. Leymore is surprised to hear the word "Caliburn." Elatha states that Cai was in possession of the Caliburn the whole time, but was unskilled at using the Caliburn. Elatha says Cai knew better than anyone to use the Cailburn with a alchemy crystal, as it would consume the user's soul. He then states that it is a curse brought upon Cai who ventured into the "forbidden domain."
Cai is seen with the Heart of Courcle and Neamhain as she attempts to merge the Cai, who is hosting the Caliburn, with the Heart of Courcle, making Cai become light itself. Leymore and the Milletian arrives after the artifacts merge and attempts to persuade Neamhain to return Cai back to himself, but Neimhain ignores Leymore's pleas and begins her plans to bring back Tir Na Nog from darkness. Cichol then appears to congratulate Neamhian for a mission well done, with Elatha by his side. Cichol announces that the purification of Tir Na Nog is something he desires as well, however through the use of "blood purification." Using Elatha as part of the pact of Noitar Arat, Elatha forfeited his destiny to save "useless lives." Elatha then reveals he knows the truth and that Neamhain is his mother. He is then ordered by Cichol to merge with the Cai and commence the destruction of the Soul Stream, ignoring his mother's pleas to embrace the light. Before Elatha merges, the Incubus gives the Milletian his Music Box and urges them to protect the Soul Stream. Cai then absorbs Elatha and gains the powers of the Goddess of Light, then proceeds to destroy the Soul Stream. Leymore tries to stop Cai, but Cai punches him and disappears. Cichol then declares the Soul Stream's destruction and attacks. Neamhain, angered at both the loss of the artifacts and her son, counterattacks, but before either deity can launch their attacks, Morrighan arrives and orders them to stop fighting, then tells the Milletian to save the Soul Stream. Before they leave, Leymore gives them a Cylinder to save Cai.
After finding Cai, who has requested Leymore's help, the Milletian goes to Sinead and asks about Leymore's whereabouts. Sinead states that Leymore was in Shadow Taillteann doing some alchemist research. However, Leymore has not been heard from in a while, and was last reported behind the Alchemist House in Shadow Taillteann. The Milletian then sets off for Taillteann's Stonehenge, in search of Leymore.
Upon arrival, various Shadow Monsters guards the gate. After subduing them, the Milletian heads for the Alchemist's House. Leymore is surprised to see the Milletian and hardly recognized them. He has yet to hear anything about Cai, but knowing him, he is probably concocting a wild plan by himself. Leymore agrees to help Cai not just as a Royal Alchemist, but as his friend. Unfortunately, the Milletian was being followed by Shadow Monsters and is ambushed, along with Leymore. After defeating them, Leymore is apparently distracted. He talks about Jenna and give the Milletian a letter from her. Leymore, disgruntled, wishes to talk to Jenna, but feels that it must wait. He then looks at the Milletian and realizes he was talking to himself and apologizes, and then leaves shortly after. The Milletian opens the letter and find that Jenna has found out the truth on what really happened on the Emain Macha Tragedy: her father was killed at the hands of the Royal Alchemists. Feeling uneasy, Jenna left Leymore because he was a Royal Alchemist.
The Search for Caliburn
After some time has passed, the Milletian meets with Sinead. Sinead has heard from Leymore and has left for Shadow Tara Rath. Sinead requests that the Milletian assist Leymore, along with Cai, to search for traces of Caliburn, or any clues regarding it. Upon arriving in Shadow Tara Rath Castle, Leymore finds the Milletian and explains his plan. The plan was to search the Castle for any traces of Caliburn may have left behind from its original location inside the castle. After some investigation the Goddess Morrighan appears before Cai, Leymore, and the Milletian. She is aware that they are searching for the Caliburn. According to Morrighan, the Caliburn was a tool used by Aton Cimeni to form the world of Erinn. After the creation was complete, it was left in the hands of a man named Partholon. Partholon created the Altar for Caliburn and faithfully guarded it. However, Partholon fell at the hands of the Fomors until the Second Battle of Mag Tuireadh. The Caliburn was return to Tara Rath Castle by Lugh, but eventually came into the hands of the Fomors once more. Caliburn must be returned to its original place on the Altar at Tara Rath Castle or peace will not be sustained. The Shadow Realm is now a threat to Erinn. Morrighan also says that Cichol knew about the Caliburn bringing Erinn to its destruction. Even the Gods can not deny that the destruction of Erinn has already begun. She says that the Caliburn has become unstable and is now forming the Sword of the Gods, Brionac. She requests that the Milletian bring back the Caliburn return it to its Altar in Shadow Tara Rath.
Leymore is summoned by Sinead, along with Cai, to help the Milletian assist Buchanan, who is currently investigating in Shadow Tara Rath Castle. Leymore feels uneasy that Buchanan is alone in the Shadow Realm. After searching the entire first floor of the castle, the group find Buchanan unharmed. He explains what he has discovered and asks them to obtain the Book of Partholon. Buchanan then says that the book is hidden by a secret mechanism found in the castle's Restaurant. He then hands group a crudely drawn map with the correct switch order. After leaving the Shadow Realm, the group then reports to Sinead and return to the Shadow Tara Rath Castle to find the book of Partholon. Leymore has written in the information down on how to operate the secret device.
Upon arriving at the book's location, the group was ambushed by Mata and he summons Shadow Monsters in an attempt to stop them. Cai attempts to persuade Mata by saying Cichol warned them about the danger Erinn may face and that it could affect both Humans and Fomors alike. Mata replies that Cichol is no longer their king and is a coward who has forsaken the Fomor Ideal. Mata attempts to attack the group, but is suddenly stopped by the Python Knight, in the name of the Holy Land. The Python Knight proceeds by eliminating the Shadow Monsters, along with Mata, with Shadow Death. Cai demands that the mysterious Python Knight reveal his identity, exclaiming he is neither Human nor Fomor. The Knight replies that he resides between the boundary of Light and Darkness and does not need to explain anymore. He looks the Milletian, seeing as they inherited the Power of the Gods. He calls the Gods as a race with endless greed. He then asks the Milletian if they wish to be a God, or just a human with human willpower, stating only time will tell. The Python Knight also says they may become a monster, which would be neither Human nor God. He entrusts the Milletian with the Book of Partholon, along with the pages. He will keep a close eye on the Milletian and vanishes back into darkness. Cai believe the the Python Knight is bad news, questioning who he is. He will attempt to research the Python Knight and find whatever he can on him. He instructs Leymore to stay with the Milletian and investigate the Parthalonian magic, leaving shortly after.
Recreating the Ancient Parthalonian Magic
As the Milletian was restoring the Book of Partholon and unlocking its secrets, Leymore was conducting Alchemy research on the ancient Parthalonian magic. The Milletian then gets word from Sinead that Leymore is nearly finished. Sinead requests that the Milletian visit Leymore, with the Partholon Crystal, as soon as they can. The Milletian rushes to Taillteann's Stonehenge to visit Leymore and assist in his research. The Milletian finds Leymore at the Alchemist's House in Shadow Taillteann. He requires a few more materials. The Fomors, at the same time, are conducting experiments in Shadow Taillteann's Square. He requires some materials from the Fomors and Shadow Monsters found in the square. The Milletian was reluctant to gather the items for Leymore. After gathering the materials, Leymore takes the items, including the Partholon Crystal, and uses the documents obtained from Buchanan to attempt casting ancient magic through the use of Alchemy. The Goddess Morrighan suddenly appears and congratulates the two for recreating the ancient Parthalonian magic through alchemy. She was surprised that it could even be done through alchemy. She warns the Milletian about Neamhain's plans regard the Sword of the Gods. Leymore is surprised to hear Neamhain's name, as she gave up her plans after Elatha's death. Morrighan says that Elatha's death strengthen Neamhain's will to carry out her plan to purify Tir Na Nog. However, Neamhain's plan will bring the opposite of what she envisions, death and destruction. The Caliburn made its way to Aer and has begun to form the Sword of the Gods, Brionac. Morrighan says they must stop Neamhain at all costs.
Leymore begins to search for Jenna, and eventually learns that Jenna was seen on Ceo Island, inside the underground spring where Aer resides. However, upon arrival, Jenna has already left and finds the Milletian, who is about to lose consciousness from Cichol's transfer of power. He calls out the Milletian's name before they completely lose consciousness. Worried, he brings the Milletian to Collen, who takes care of the Milletain, then shortly leaves after he confirms that the Milletian will be okay. After the Milletian wakes up, Collen asks the Milletian to stay until he came into contact with Leymore. Collen soon receive a message from Leymore. Leymore did not explain the situation, but Jenna was sighted in the Shadow Corrib Valley. Collen requests that the Milletian help Jenna, if they can. The Milletian goes to find Leymore by entering Tara's Stonehenge.
Upon arrival, Leymore is glad to see the Milletian almost fully recovered. Leymore suspects the Erg to be coming from Shadow Corrib Valley's waterfall on the western side. The Erg may have come from Neamhain's ritual to purify Tir Na Nog with the Brionac. Leymore begins to have an uneasy feeling that Jenna may be in danger. Heading westward, toward the waterfall, Leymore and the Milletian finds Jenna, who is currently unconscious, undergoing the ritual Neamhain set up. She does not want them to interfere. Leymore questions Neamhain about Tir Na Nog, who is it for, and what benefit will humanity gain from Tir Na Nogs revival. To protect Jenna, he stands up against Neamhain. Neamhain praises Leymore's valor, but calls it foolish and weak. Leymore attempts fight Neamhain as the Milletian attempts to grab the Brionac. Using the alchemy of Shock, the Milletian manages to distrupt the Brionac and Neamhain's ritual. Leymore's efforts fail against Neamhain and Jenna suddenly realizes what she has done. She then threatens Neamhain for what she has done to Leymore. Neamhain now questions Jenna's allegiance to her, stating that Jenna would give up everything for a "worthless human emotion." Jenna finally understands her past and hopes for the future. Neamhain says Jenna is chasing a fleeting illusion and leaves. Jenna then give the Brionac to the Milletian, feeling it would be safe with them as Jenna tends to Leymore.
Leymore, Jenna, and Cai arrive at the Altar of Caliburn. Leymore and the others had trouble with Partholon's Barrier. Upon their arrival, the group finds the Milletian surrounded by the Python Knight's minions and offers to take care of them while the Milletian takes care of the Altar of Caliburn, returning Brionac to its rightful resting place. By doing so, the Milletian removed all the Parthalonians, including the Python Knight, from the area around the altar. Jenna begins to think about how it was all started over the Tuan's selfishness, and how it affected his thinking. Cai finds that the Shadow Realm still exists, even thought the Caliburn is now in its rightful resting place. Leymore suggests that the Shadow Realm will continue to exist and it is something that can not be undone. Leymore also says that there is still a chance to choose, hoping that is enough. The group of four is seen walking away from the entrance of Shadow Tara Rath Castle, presumably to the Stonehenge to take them back to the real world.
Secret Waterway Investigations
Leymore is contacted by Sinead to investigate the site of the Homunculus Experiment conducted by Jarlath. The Milletian is to aid Leymore in any way they can. Upon arriving inside Shadow Tara Rath Castle, the Milletian is greet by Leymore. Leymore hears that the Milletian has spoken to Lennox. To his dismay, he admits that Lennox is his father. At some point, Leymore cut off all ties with his father and has not spoken with him since he renounced any relationship between him and Lennox. The reason behind this was the truth about the Tragedy of Emain Macha. Leymore learned that the Alchemist Regime was responsible for the tragedy that occurred for that faithful day, causing a genocide of Druids, and anyone related to Druids. Lennox had the power to stop the Corrupt Alchemists by giving the order to the Royal Alchemists. However, Lennox never did such a thing and let the tradegy progressed as it did. According the Leymore, Lennox did nothing in order to maintain poilitcal power over the alchemists, saying the being an Elite Alchemist can lead to cold-hearted bloodshed. Leymore then appoligizes to the Milletian for getting out of hand, delaying their time to investigate the Underground Waterway, explaining that the tension between the Royal Alchemists and the Corrupted Alchemists is worse than it used to be. Leymore obtained a tip that a Corrupted Alchemist by the name of Amos has been sighted inside Shadow Tara Rath. The Milletian agrees to help Leymore pursue the Corrupted Alchemist.
As they search for the castle for Amos, Amos sees Leymore and the Milletian and cuts them off with a metal gate. Leymore was conviced that it was Amos. Leymore conducts a plan to chase Amos by letting the Milletian chase him while he attempts to cut Amos off. As the Milletian chases Amos, Leymore attempts to cut him off. Soon the Millitain was able to lead Amos to Leymore and begins the interrogation. Amos reveals that the Corrupt Alchemist has developed a new Alchemy technique that utilizes the pressure built up in a cylinder and can be used create an explosion. The name of the technique is called Heat Buster. Amos then reveals that the Homunculus Experiment is nearly complete. Leymore will return to Tara Rath Castle, with Amos in custody, and report his findings. Leymore requests that the Milletian investigate the Underground Waterway on their own. According to Amos, a large Homunculus Experiment took place recently and may be related to the transmutation to Claimh Solas.
The Alchemist War
Leymore and Jenna has gotten word that the Royal Alchemists are about to confront the Corrupted Alchemist, beginning to start a war between the Factions. Leymore explains the the Royal Court has ordered the Royal Alchemists to eliminate the Corrupted Alchemists. The Milletian agrees to help them both and head towards the square, where the war begins to escalate. Upon arrival, they are greeted by Lennox. Leymore, still disagreeing of Lennox's use of Alchemy, explains that he is only helping as his duty as a Royal Alchemist and nothing more. Lennox is still not convinced about his son's desertion. Cai then butts in, telling the two family members to stop fighting and worry about more important matters, such as taking care of the Corrupted Alchemists.
As the battle draws to a close, the Milletian, Jenna, Leymore, Cai, Lennox, and the Royal Alchemists corner Helvetius. As a finality act, Helvetius overloads all the nearby Alchemy Ovens and causes them to self-destruct. The group begins to escape, running away from the fierce flames produced by the self-destructing ovens. Jenna trips near an oven that has yet to explode. Lennox, realizing that it will soon self-destruct, runs to Jenna's aid and places a Barrier Spike close to Jenna, shielding her from the explosion. Lennox was caught in the blast, as he was too close to the explosion, and is fatally injured. Leymore then calls out to him and rushes to his aid. Lennox hoped that Leymore would someday understand why he uses alchemy the way he does. He regrets that he should told his son sooner, then asks for his son's forgiveness with his dying breath.
Fragments of Falias
Morrighan had summoned the Milletian, Leymore, Cai, and Jenna to the Underground Spring in Ceo to meet with her. She explains by finding all of the lost treasures left by the God when they descended into Erinn, the Brionac was completely restored. She tells the Milletian to use the light of the Goddess to shine the path to Holy Throne of Falias. Morrighan then gives her blessing and enchants the Brionac, but falls due to her wounds against her battle with Nuadha. Leymore and Cai rushes to Morrighan to assist her. The Milletian does the same, but is stopped by Jenna, who tells the Milletian that as the Master of the Brionac, only they can stop Nuadha and thwart his plans on becoming an all powerful god. The Milletian heeds Jenna's words and leaves to stop Nuadha once and for all.