Betrayed by his superiors and left for dead, XIII has definitely left the secret service in favor of a wandering life. In the hope of finding food and shelter, he went to Empire City and meets Betty Barnowsky, a beautiful activist involved in the fight against the major energy groups. Betty saving a police raid muscled XIII calls within the Veil, an underground organization led by Max Vargas. Veil attempts to expose openly the climate research center Hearpe (High Energy Auroral Refraction Protonospheric Emitter), whose real purpose is to influence the climate for economic reasons. Betty seduced both by itself and by his speech committed XIII agrees to help activists.

Headquarters of the multi-national Synequanon are bombed, resulting in the passing of innocents. Authorities and the media hold The Veil and XIII responsible and label them as terrorists. XIII is captured and tortured by a mysterious figure, who seems to know him intimately.

On the eve of the American election, XIII is hunted by powerful enemies: the Government, which now realizes he was never terminated; Synequanon, clamouring for revenge for the bombing of their headquarters; and by the mysterious figure who is after a set of equally mysterious letters. While evading these factions, XIII seeks to unravel the mystery behind the letters.

Caught in the permanent storm surrounding Ariella Island, XIII is shipwrecked. Posing as a fisherman, he is befriended by Dr. Westlund who holds critical information about the letters. The aging scientist and his daughter Gale hide XIII from the Synequanon security forces holding them prisoner. On the mainland, Harriet Traymore wins the presidential election but Carrington refuses to leave office.

XIII and Amos grapple physically and mentally, as they try to uncover the truth behind the bombing of Synequanon's headquarters. Fueled by grief and rage, Amos tortures XIII's body and attempts to manipulate his mind. XIII strives to prove his innocence and escape from Amos' twisted grasp.

XIII crashes an ultra-exclusive birthday party to find the final letter. The host of the party, and the owner of the letter, is a Russian Oligarch with a penchant for collecting expensive items such as rare weapons and beautiful women, and using the former on the latter. Part of his collection includes one of the Tesla letters, and XIII finds he isn't the only person who's come looking for it.

XIII, Betty and Mozambique rush to free Vargas before he's deported to Guantanamo, as they believe he must have information about the letters. Synequanon's tests of their newest technology have unforeseen, cataclysmic results.

Betty and XIII both question the reality of their situations: concealing his true identity, XIII sails to China, searching the ship for the final letter which has been hidden somewhere on board; Betty is abducted and delivered to her father in London, who claims that her experiences with XIII and the Veil have been nothing but the narcotic-induced hallucinations of a runaway.

X111 is captured by the Xu Corporation and they figure out that he is not Victor Gong, but he acts, thinks and acts like Victor. This raises questions. Pong manages to get the last Tesla letter from X111 who remembers the memories of Victor Gong also with the help of his daughter. Meanwhile Mozambique gets captured. Carrington imposes a state of martial law halting the transfer of power to Treymore.

Xu Corporation gives XIII the face of agent Victor Gong (XIII.2), which only intensifies his struggles with identity. Betty plots revenge against her father by trying to sabotage his efforts in China. Carrington watches his empire crumble around him.

XIII is thrown into The Pit, an underground dungeon where prisoners are forced to fight to the passing in matches broadcast live online. XIII tries to rally the prisoners, which include Amos, Mozambique and Grier, while staying alive long enough to attempt an escape. XIII.2 and Betty mastermind a hostile takeover of Xu Corporation.

XIII, Betty and Amos escape from The Pit and into Shanghai but are trapped in a mysterious and sinister riot that has spontaneously formed around them. Thirteen-year-old Yen-Boi and his father Ping help them find and fight their way through the chaos. With access to a Navy Seal helicopter, Amos leads them towards the extraction point. Carrington is pushed further into the bunker by Traymore's forces, and makes a last-ditch effort to rally support.

The safety of the world is at stake. The Chinese HEARPE is now fully operational. With the help of Betty and Barnabis, XIII tries to destroy HEARPE while XIII.2 attempts to unleash its destructive force - a terrifying array of natural disasters - on the United States. But only one man will triumph. Only one man will survive. Making his last stand in the bunker, Carrington contemplates extreme measures.