Blue Boy is a hybrid of beat-em-up and shoot-em-up, and is a pioneer of the modern 'tower defense' game. Players assume the role of the flying superhero 'Blue Boy' and fly around the world to stop alien attacks on major cities.
The objective of each level is to stop the aliens from abducting residents wandering around the level; Blue Boy can fly freely around the level and use weapons such as punches and lasers to eliminate the alien threat. If the aliens manage to capture a human, the player must quickly eliminate the captor before they both fly out of the level. Enemies can appear anywhere, so, as in 'Missile Command', the order of response must be carefully considered. Some aliens will attack the player directly rather than abducting humans. Humans who are freed from their abductors are released from their cocoons and gain bonuses such as additional weapons, smart bombs and extra lives, but in doing so may be distracted by other abductions in progress.
Once all aliens have been eliminated and no humans remain, the attack is complete. Each city has two waves of attack and a boss battle with a spaceship. The game ends when Blue Boy is eliminated or all humans are abducted; a mini-map similar to Defender allows players to keep track of aliens and humans in the level.