- The game is structured around 5 new missions and a subplot based on the Spies' daily life:
- Mission 1 - Secret agencies are attacked all around the world - the spies have to discover who is responsible to prevent the WOOHP (Jerry and Spies' agency) from being destroyed.
- Mission 2 - A love elixir drives high-school students crazy - the spies have to act quickly to bring peace and harmony back between lovers.
- Mission 3 - A former WOOHP secret spy cloned the best agents to create her own army for her new brand secret agency - Alex, Clover and Sam have to stop her before they get cloned.
- Mission 4 - An MMORPG changes Guild members into diabolic creatures - the girls have to find the Guild leader and stop him from hypnotising innocent gamers.
- Mission 5 - Jerry is missing - the spies have to investigate in a sub-marine military camp to find his trace and save him.
