Two years ago, Shibuya was ravaged by a biological terrorist attack using the deadly Ua virus. Maria Osawa was saved when her father inoculated her against the virus, but is left with partial amnesia from the shock. She works as a cameraman when she reunites with a girl named Canaan in Shanghai, China. A gifted assassin with synesthesia, she is under orders from an unknown organization for a yet unspecified mission
Canaan, a covert agent with the power of synesthesia (the ability to combine senses), arrives in China just in time to save her friend, the young photojournalist Maria Osawa, from a deadly attack by the terrorist organization known as Snake. But Canaan has tenuous ties to various Snake operatives, which places Maria in peril.
As Minorikawa realizes Maria has a connection to the mysterious assassin Canaan, they are attacked in downtown Shanghai by a mysterious old man and his young accomplice. But as they are on the run from the dangerous duo, Canaan comes to their rescue, provoking a dangerous revenge.
When Canaan kills an old man who is threatening Maria, she provokes a young mutant to murderous revenge. So as Maria and Canaan enjoy their reunion, the evil boy plots a terrifying plot to kill Canaan as penance for her sin of killing his friend. Meanwhile, Minorikawa finds the mysterious Hakko may know more than Santana will allow her to admit.
Rescued by her "sister" Liang-Chi, and now taking her place of power as the leader of the terrorist organization Snake, Alphard sets a trap for Canaan, luring her out into the open at a glamorous state dinner. Once there, Alphard reveals she and Canaan have more in common than Canaan ever let on.
As Alphard makes preparations for her attack on the global anti-terrorism conference, Liang-Chi devises plans of her own. Blackmailing Yun Yun with the threat of withholding medication she needs to survive, Liang-Chi coerces her into killing Canaan, using Maria as bait. Meanwhile, Minorikawa attempts to get closer to the mysterious Hakko, despite Santana's efforts to keep them apart.
Minorikawa and Maria receive an invitation to attend the anti-terrorism conference, but it's only a ruse by Alphard to lure Canaan to the summit. Once there, Liang-Chi and Alphard launch their attack, sealing the world's key diplomats in an office chamber, infecting them with the Ua virus--and causing Canaan to rescue Maria, putting her own life in danger.
After the Ua virus is unleashed, infecting world leaders, the global governments have no choice but to allow Alphard to drop a bomb on the anti-terrorism conference, killing millions. But as Alphard deals with the US government, Canaan sneaks into the summit to rescue the captive Maria and stop the imminent air strike.
After Alphard chooses Canaan over Liang-Chi, the spurned terrorist breaks off and vows to exact a terrible revenge. Meanwhile, Minorikawa confronts Santana, and is at last allowed to get answers from the mysterious Hakko. Canaan tries to adapt to the fact that she has lost her powers.
Canaan, Maria, Santana, Hakko, and Minorikawa head to the desert to discover the secrets of the Factory. Once there, Santana confesses his involvement in the massacre, and Hakko reacts with dangerous emotion. Possessed by jealousy and descending into madness, Liang-Chi makes a deadly attack but finds her rage thwarted by a surprising adversary.
When they enter the Factory's deepest chambers, Canaan, Maria, and the others find the diseased survivors of the horrible experiment. There, Hakko is confronted with her own horrible past, which gives Liang-Chi the advantage she needs to attack the group from within.
As Liang-Chi's subversive plan takes a deadly toll on the group, Canaan and her companions struggle to escape before more lives are lost. Meanwhile, Natsume and Alphard reveal they have a common connection to the Ua virus and the mysterious Factory. But when Liang-Chi discovers she cannot reclaim Alphard's love, she makes a tragic decision.
Alphard kidnaps both Maria and Yun Yun in an attempt to trap Canaan into a deadly confrontation. As both girls hurtle toward certain death aboard a runaway train rigged with explosives, Canaan risks a daring rescue. But when she is confronted by Alphard, she discovers a terrible secret that threatens her very soul.
After saving Maria and Yun Yun from Alphard's trap, Canaan decides to end their rivalry once and for all. And when Alphard finds out Canaan's inner truth, her own existence is shattered--as is her perception of their mentor and what he meant to them both.
