Jack and Rowe board an airship to investigate the proposed illegal sale of a replica "mermaid’s foot", an Ishtar sacred object. The royal family is trying to remove these replicas from the market and Jack and Rowe suspect Professor Freud and his assistant Linda are the sellers. Jack and Rowe fake the death of their buyer, but Freud and Linda implement an elaborate plan to pretend the object was stolen from them. However, Jack and Rowe are not fooled and Linda, a professional bodyguard, attacks Rowe, but they are defeated and caught.

International actor and Cloud 7 agent Moriya Kou, is abducted by the Schwartz Stravinsky of the Hornet crime syndicate to find the location of the Empest Conference and assassinate the world's intelligence bureaus' chiefs. Jack and Rowe infiltrate Hornet headquarters and free Moriya, but they are captured and then try to cause confusion about the real location of the conference. Moriya is a actually double-agent, and after overhearing Jack and Rowe communicate with Cloud 7, he signals the location to Stravinsky who then sends his forces there. However, the information is incorrect, and when Stravinsky and his forces arrive at the false location, they are surrounded and captured by Ishtar troops.

Jack and Rowe are introduced to Commander Camille and asked to escort Noelle Adelaide, one of the reject "15-year Princess" candidates, back to Ivory Island in the utmost secrecy to avoid the media. On the train journey to the island, they encounter Drisden, the rude director of the Ivorystone mining company. Noelle reveals that her grandfather is the caretaker of island's iconic clock tower which has been damaged in a recent storm and the island lacks funding to repair it. Jack and Rowe deposit Noelle at the railway station, but she returns to the capital and begins busking to raise money for the island’s clock tower.

Actor Eric O’Connell is killed by the sniper Gray F. Stratos, known as Tear Drop, while on board a cruise ship. By coincidence, Rowe encounters Stratos' daughter Leila at a city fountain and takes her to Cloud headquarters. Dez plants a bug under her cup and when she returns home, Cloud 7 learn that Gray's target will be at a banquet. However both his daughter Leila and Claire are captured. At the banquet, Jack and Rowe discover that they are the targets, but they avoid being shot. They determine that Gray's employer is the crime boss Dice who has abducted Leila and Claire, and Jack goes to rescue them while Rowe goes after Gray.

After a building explosion at a mining facility, the DTI corporation announces that it was caused by a malfunction in a cooling system. Jack and Rowe receive a tip off from Mark/Margaret that the explosion was deliberate, then DTI's executive director Taylor's car is bombed and Cloud 7 suspect the bomber called Angel. They are assigned to investigate, however Frost, Director of DTI's Information Management Division, says that they will handle it themselves. Nevertheless they examine a bomb threat note, which the DTI executive Claudia suggests means Sunday at midnight. Jack reveals to Rowe that he and Claudia were partners some years ago, but suspects that she is the bomber. She admits her attack on DTI because of its unprincipled practices, but she is then shot dead by one of their agents.

A bomb explodes in a tower of the royal palace and Duke Regent Rand falsely announces that it was caused by an electrical fault. Commander Camille berates Cloud 7 for not apprehending Angel and preventing the bombing. Jack and Rowe examine an Ivory Island nursery rhyme which appears to provide clues to the bombings, and travel to the island. While ejecting Drisden from Tola's tavern, Jack and Rowe again meet Noelle. They realize that Ishtar and DTI make all the profits from Ivorystone mining, leaving the islanders with only their salaries to sustain them. Meanwhile, Duke Regent Rand realizes that Noelle really is the 15-year princes, and Istar troops attempt to capture her. Jack and Rowe fight them off and Camille lands on the island and acknowledges Noelle as the princess.

Jack and Rowe are assigned to deal with Stephen Vincent, a crime syndicate courier, while Noelle is moved into the royal palace. The two agents also note that Noelle is also referred to as Angel, and the bombings have ceased since she moved to Ishtar. Meanwhile, Jack and Rowe track down Stephen Vincent and attempt to recover the Midnight Sun Emerald in his possession. They broadcast details throughout the palace which helps trap his accomplice Dent, when he arranges to meet Stephen Vincent to pick up the gem. He is caught by Jack and Rowe, however his girlfriend Matilda actually has the gem, and with Claire's help they apprehend her as well.

Claire masquerades as Noelle at a baseball game so that Jack can take Noelle on an outing. Meanwhile, Rowe becomes trapped with a group of passengers in a cable car with the diabetic father of the great player, Maurice Butterfield. Through a great team effort, Rowe and the passengers manage to retrieve a medical package sent along the cable and save the sick man as well defusing a bomb on the cable car.

A news item explains that Prince Spada Freed was imprisoned on charges of murdering his younger brother, and his wife Ciel Sado disappeared, the love between them transcending the rivalries between the two royal families. Noelle is still adjusting to her role as a princess, and Rowe realizes that she is not Angel, the bomber. Meanwhile there is mounting suspicion over Mister's meeting with Taylor from DTI during the baseball game. Rowe encounters one of the passengers from the cable car, which leads to an Ivory Island resistance group who he suspects is Angel. He lays a trap and apprehends them before they can detonate a bomb at a ceremony at which Noelle is the guest of honor.

Mercenary Jude McManus is hired by DTI and proves his worth by defeating Rowe Rikenbacker, meanwhile Mister also joins DTI. Cloud 7 is removed from guarding the princess and DTI is given the task of protecting her. Later, Mister orders Rowe to kill princess Noelle on the day of her coronation. Coincidentally, Claire declares her love for Rowe and they kiss for the first time.

Taylor of the DTI holds Mister Pennylane and Dez captive as he waits for Rowe to assassinate Noelle on Pennylane's orders. Meanwhile Camille receives information that the sniper Gray F. Stratos has entered the country. On the evening of the coronation, Noelle speaks to the people of Ishtar, telling the story of her heritage, but also how Duke Regent Rand made a secret agreement with DTI to jointly exploit the Ivorystone deposits. Suddenly Rowe rushes forward and shoots, and Noelle falls to the ground.

The citizens are shocked by Rowe's shooting of Noelle, although she is still alive. Rowe is caught and Taylor then announces that the assassination plot was carried out by the Royal Houseguard under the orders of Mister Pennylane. However, Camille reveals that the man captured is actually Taylor's own son Frost whom Jack and Rowe have disguised as Rowe. Pennylane also accuses Taylor of conspiring with Duke Regent Rand to frame Prince Spada. Panicked, Taylor sets of a series of explosions and escapes in the confusion, but he is caught by Jack and Rowe although he is shot by the sniper Stratos, as a public service and for earlier abducting his daughter. A short while later, Noelle has recovered from her gunshot wound and flies over Ivory Island which has a new clock tower, and where the mining lease is now controlled by the royal family. As Rowe is walking home with groceries, he is stabbed from behind by Frost, however Jack arrives and shoots Frost.