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.

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.

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.

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.

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.

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.