It is a rainy night at the Legacy House. Kristin is sleeping in her chair, troubled by chaotic dreams of horses, knights, a strange stern-faced king, a little girl, and always coming back to a crucifix on a chain. A man is calling her name in her dream, which blends into Derek gently calling her. "Are you all right?" he asks, concerned. She passes it off as too much late night reading, indicating to the book open on her lap with the picture or a Knight Templar on horseback. Derek has brought a package that had just been delivered by courier from her brother Ethan. Inside is another package -- a map tube -- and a note from Ethan that he had gone home on semester break and found this waiting there for her. Derek, examining the map tube, says the postmark indicates it originated in Istanbul two months previously.
They discover an old map inside, in an unknown archaic language, and (unseen by Derek who is preoccupied with the map) a piece of paper with a symbol like a capital A on it. It causes Kristin's eyes to widen -- in shock? surprise? - and she immediately conceals it from Derek. "That's not paper," she remarks of the map, and wonders if it might be parchment or sheepskin. "Or human skin," Derek remarks, shocking Kristin, and he tells her he's seen it before ("Twelfth Cave" in season 1). "Lovely, a medieval Hannibal Lecter," she remarks. He suggest that she let Alex scan it into the computer. "And you don't have any idea who might have sent it?" he asks, and she replies no, but looks troubled.
Later when she is alone in her room she runs the seemingly blank sheet of paper over a candle flame. Secret writing is revealed:
signed with a symbol resembling a capital A with a tail on the left leg and a crossbar at the top. She burns the note, and fingers the crucifix around her neck, perturbed.
In the Control Room, Alex has the image of the map on the screen and pronounces it genuine as far as she can tell, circa 1300 AD. Derek remarks that that coincides with the Crusades, yet it does not appear to be a map of the Holy Land. Alex confirms that it is indeed made of human skin, causing Kristin to abruptly drop it back on the table and exclaim that it's barbaric. "Or an act of faith by someone who valued the map more than life itself," Derek says. Alex also informs them the writing is in archaic French, but in some kind of code. Kristin notices a design on the top left corner, which Derek identifies as a shield with a crusader's crest, probably belonging to the man who drew the map. It could, he theorizes, be a map to the Holy Grail, considered by the Knights to be so holy they would rather die than reveal where it was hidden. Kristin remembers Jacques De Molay, the last great leader of the Knights Templar and, Derek informs them, a member of the Legacy. He was accused of stealing the chalice and put to death in 1314 by Phillipe of France. The Legacy believed that Phillipe had made a pact with the dark side and killed De Molay for refusing to reveal the hiding place of the chalice.
"So it's still out there somewhere..." Kristin speculates. "In theory. All you have to do is find it," says Alex, and Kristin thinks of the secret note.
Kristin is waiting anxiously in the lobby of the Hotel Metropole in Istanbul a day or two later. She is startled when a guide, Mr. Ali, comes up behind her and offers his services as tour guide, which she politely declines. After Ali leaves a mysterious robed man wearing an eye patch comes up behind her and orders her in a raspy voice not to turn around. He refuses to tell her who he is, and demands to know if she has brought the map. She answers yes, but that she doesn't have it on her but put it somewhere safe. He tells her to bring it at 5pm the next day to the Well of Souls. She demands to know about her father, Justin Adams, where he is and if he is all right, but when she turns the man has disappeared.
In San Francisco Nick, Derek and Alex discover that Kristin has taken the map and left without a word to anyone. Nick has found and successfully reconstructed the note Kristin had burned, and Derek's suspicions are confirmed when he deciphers the signature symbol as JA - Justin Adams. As he and Nick prepare to leave immediately for Istanbul, Alex stays behind to work on the (computer copy of) the map.
In the hotel in Istanbul Nick bribes the hotel clerk to reveal information on Kristin's whereabouts. He tells Nick that she asked how to find the Well of Souls, and even though he had told her it was a bad place she insisted, so he found a driver for her. They are only an hour or two behind her, and he gives Nick directions.
Kristin and her driver arrive at the Well of Souls, a circular depression surrounded by a low rock wall, with a slab carved with Templar crosses. Kristin calls for her father, and even though she had told him to wait the frightened driver quickly drives away. As soon as he is out of sight Kristin is confronted by a tall, angry blond man with a dirty face, dressed in robes and a crown. Speaking in French he demands the map; Kristin insists she didn't bring it, and he grabs her around the throat and demands more forcefully. She tells him to go to hell. Just then he sees her crucifix; this seems to anger him and he strikes her to the ground. He stands over her as she lies there unconscious.
Nick and Derek arrive very soon after this and find her barely conscious. There is no sign of the strange blond man. As they help her into the jeep and drive away, they are watched by the one-eyed man.
Back at the hotel that evening Derek presses brandy on Kristin even though she doesn't drink, insisting it will help her sleep, then waits for an explanation. She tells them that her father was missing for so long that she got tired of all the waiting and wondering, not knowing if he was alive - she had to come. Derek asks her about the note Nick found in her room, and she explains she knew there would be secret writing as soon as she saw her father's mark - it was a game they had played when she was a child. When Derek admonishes her that she should have told him, she explains that the note instructed her to come alone and she just couldn't take the chance.
Her attacker spoke French, she says, and had a sense of evil about him that she's never known. She didn't give him the map because it is the only connection she has to her father. Derek points out that it could all be a trap and her father could be dead, but Kristin firmly rejects that. She is convinced he is alive, that she feels it even stronger there in Istanbul. While she was lying on the ground almost unconscious, she remembers hearing someone speak, and while she didn't recognize the voice he knew her name.
Derek offers to escort her to her room, but she turns him down. She tells him with sincerely that she truly appreciates them coming, but there are some things she has to do on her own. Derek assures her he understands. But when she leaves he tells Nick to make sure she gets to her room.
She confronts Nick in the corridor: "Need help finding your room?" He admits when challenged that her slipping out had crossed his mind. Remorsefully, she tells him, "I really hated deceiving you, but it's hard to explain what it's been like for me the past two years." "A big hole in your heart, can't fill it no matter how hard you try?" Surprised, she realizes that he does, indeed, understand. Kristin supposes this will end her career with the Legacy, but Nick assures her that if disobeying the rule book was such a big problem then he's sure he'd have been out of a job years ago. Reminding her to lock her door, they say goodnight.
Derek phones Alex to let her know they have found Kristin, that it was close but she's all right. Alex has discovered the shield on the map is De Molay's. Phillipe IV had him and all members of his order arrested on Friday, October 13, 1307 (ed. note: this is the source of the superstition about Friday the 13th being unlucky). He believed the Templars had found the chalice and he wanted to know where it was hidden. When De Molay refused to tell, Phillipe had him burned alive. Derek knows the rest of the story: De Molay cursed Phillipe to follow him in death and never reach heaven, and the king did indeed die within the year. If the curse worked, then he's been walking the earth for 700 years. De Molay's ashes were scattered to the wind. As for the map, Alex is comparing it with existing topographical features. When she asks how Justin Adams fits in, Derek reports that the DNA expert was called in to test a map purporting to have been written in De Molay's blood - maybe this map - that had surfaced in Istanbul. He disappeared before he finished, and was rumored to have had his throat cut and his body burned beyond recognition. London decided not to tell Kristin because it was unconfirmed.
Kristin dozes fitfully, still fully clothed and lying on top of her bed. She keeps flashing to the crucifix and Phillipe, and is brought back to awareness when a badly burn-scarred hand covers her mouth. It is the man with the eye patch who agrees to take his hand away if she promises not to scream. He was the one who sent her to the Well of Souls, she asserts, and he confirms it. When she demands to know about her father, he tells her to give him the map and he will take her to him. She agrees, knowing she has no real choice but to trust him.
They drive out into the desert with the map, the strange man always careful to keep his face obscured. Even though the forests and castles are gone, he says he can go by features that still exist - they need to go up into the mountains if the map is correct. She wants to know why her father did not come himself, and he tells her that he was afraid his presence would bring her harm from the soulless spirit who attacked her - all that is left of King Phillipe. He pursues her father because of the pact made with the dark side when he was still king, to find and destroy the chalice, but he has always underestimated the power of the chalice to protect those who believed in it. "You must have faith," he tells her. She can't understand how a man can give up everything including his family to pursue something that might not even exist, and not even say goodbye. "Sometimes a man must do things that people he loves won't understand," the man says. "Finding the grail, clearing the name Jacques De Molay has given his life purpose." He sacrificed everything for what he believed in. "Including his family," Kristin says, bitterly.
Derek receives Alex's fax of the map with the modern coordinates when Nick comes to tell him that Kristin is not in her room. There is no sign of a struggle so she appears to have gone willingly. Alex has traced out a route she was able to discern from the map - east of Istanbul, along the Black Sea to the Church of the Rock where De Molay purportedly hid the chalice, and where Kristin hopes she'll find her father.
Stopped in a ravine with an overheated engine, Kristin is impatient and angry. The one-eyed man reveals the map leads to the Church of the Rock and the Grail. There are many interpretations of the map, but he believes he'll find it this time because "all quests must end." Her father, he says, will meet them there if he thinks it is safe. At this point a peasant leading a donkey comes by, and the robed man asks him for water. The man then quizzes Kristin about her father, saying she must surely know that he cared about her and was with her "in spirit." He tells her that her father loved her, and that having other commitments does not mean he loved her less, and she grants him that. Sadly she tells how she hoped after every trip into the field he'd stay, but he never did. Then when she was fifteen he just went away and never came back. Unable to hold back her tears, she tells that her mother waited and waited, always sure that this was the day she'd open the door and he would be there. When the robed man says her mother is very strong, Kristin reveals bluntly that her mother is dead - and he looks shocked and saddened, and asks gently how she died. A stroke, Kristin says, but she believes it was really a broken heart. That is why she promised herself she would find him and tell him - one of many reasons. The robed man pays the peasant for the water, and they get in the car and drive away. The peasant turns to leave, and runs right into the angry spirit of Phillipe, who strangles him to death and glares after the vanished vehicle.
Nick and Derek have stopped, and as Nick examines the ground Derek recites something aloud. "Is that Latin for call AAA?'" Nick asks, and Derek informs him that it is the crusaders' prayer Alex found on the back of the map. Nick tells of an oil leak and worn tires; they should catch up with them by nightfall. Derek thinks Kristin could be in danger, possibly even from her father. He was already acting erratically when he disappeared, and London was afraid he might have turned to the dark side. They thought he might try to contact Kristin, which was why Derek encouraged her to stay in San Francisco; London wanted him to keep an eye on her. When Nick asks if London knows they're there, Derek says no, that he couldn't chance them sending someone else who'd only get in the way. "I hope this doesn't make you feel paranoid," he jokes. "Just as long as you don't say Trust me,'" Nick answers. "Anything more I should know about right now?" "No, not a thing - trust me."
Kristin and the one-eyed man have found the Church of the Rock, the last bastion of the Knights Templar - a hole in the rocks and a rusty, very old sword stuck in the ground at the entrance. At her query he tells Kristin her father will find them. Inside he lights a torch, then some wall sconces, to reveal murals of saints and Templars, and arched niches with statues, just as the crusaders had left it. Kristin is awed. The chalice is not in sight, however, but De Molay's helmet is sitting on a stone block, inscribed with his battle cry "Beauseant." Kristin again asks where her father is. "Very close, as he's always been," is the cryptic answer. He asks her for the cross around her neck, which has a small splinter of wood inlayed on the other side, supposedly from the Cross. It protected her from harm at the Well of Souls, he says. It is the key to the chalice. "How did you know?" she asks. "Your father gave it to you when you were seven years old. You were wearing a blue dress, and you cried." Kristin finally recognizes the robed and scarred man as her father, and he at last uncovers her face for her to see.
Derek and Nick stop again to take coordinates. Nick is curious why Phillipe doesn't just take the map and find the chalice himself, and Derek points out that having the map and interpreting it are two different things. Also, the chalice cannot be destroyed on hallowed ground (implying someone else must move it for Phillipe to get his hands on it). Nick then discovers the body of the man with the donkey, and Derek "sees" that Phillipe was responsible.
Kristin tenderly examines scars of burning and a jagged knife wound on her father's throat. He mourns the time he was caught up in a fool's quest, time he should have spent with them, but he couldn't stop himself or let it go. There are evil forces that want to attack the chalice, and Phillipe is the worst of the dark ones. He was the one who gave Justin the scars, trying to get him to reveal the map. This was why he sent it to Kristin, knowing she was the only one he could trust not to betray him and would bring it back. He didn't explain in the beginning because she was safer not knowing. The time he stole from her, her mother and Ethan he can't give back; she has a right to hate him, he says, but he asks her to try to forgive him. She doesn't hate him, she reassures him, emotionally; whatever he's done he's her father, and she loves him. They embrace, and don't see Phillipe enter. Kristin removes her cross and gives it to Justin. It gave her strength and faith in him, she says. Reverently he places it in the stone, which slides apart to reveal the chalice as Phillipe watches.
Derek and Nick have arrived outside and discover the car - and the sword. Nick notes how the Crusaders were soldiers, and that this was a great place to defend a position.
In the church, Phillipe attacks Justin, breaking his back. Dropping him to the floor he grabs the chalice from Kristin and disappears out the door. Justin tells the frantic and tearful Kristin that things are beyond their control; to be brave, and know that there was never a time he didn't love her. Then he dies, and Kristin weeps over him.
Phillipe materializes before Derek and Nick. Derek pulls the sword from the ground as Nick pulls his gun. Phillipe demands (in French) that they let him pass. Nick shoots several times, with no effect, and Phillipe tosses him aside. Derek fares no better, and is also knocked down. But holding up the sword as a cross, he begins to recite the Latin prayer of the Templars, and commands Phillipe stop in Jacques De Molay's name. Kristin, hearing this commotion, grabs one of the Templar's spears and rushes outside where she thrusts it into Phillipe's side. The vengeful spirit tosses this aside also, and grabs Kristin.
Inside the church, a heavenly light shines from the mural of Jacques De Molay's shield and falls upon Justin's body. A horse appears from nowhere, and Justin opens his eyes. Outside the entrance Phillipe is threatening to kill Kristin if they don't let him pass, but Kristin urges Derek to refuse.
Justin, kneeling now and in the garb of a Knight Templar - scars and eye patch gone - prays for Jacques De Molay to live through him, that he may rise and smite Phillipe. Light shines down on him from above as he pulls the cowl of his white Templar robe over his head.
He appears suddenly outside the entrance, mounted on the horse and with the Templar robe flaming, shouting De Molay's battle cry, "Beauseant!" He forces Phillipe to release Kristin and retreat back into the Church which begins to come down on top of him. The chalice glows in his hand and he drops it as the roof collapses. Derek, Kristin and Nick watch the destruction in awe, the horse rears and Justin looks down at Kristin and nods. She gazes back in wonder, as he and the horse are transformed into a bright light and ascend into the sky.
"For a long time we stood there, staring into the darkness. No one moved. No one spoke. I remember hoping that somehow my father would reappear, but in my heart I knew. He had done what he set out to do and had paid for it with his life. Whatever dangers lie ahead, I pray my courage equals his."