"Mobile Suit Gundam Side Story: The Blue Destiny" is a manga series set in the Universal Century timeline of the Gundam franchise. The story revolves around the experimental EXAM System, a cutting-edge technology designed to enhance mobile suit performance by integrating the consciousness of a Newtype into the machine. The narrative primarily follows Yuu Kajima, a skilled Earth Federation pilot, who becomes entangled in the development and consequences of this controversial system.

The EXAM System is developed by Dr. Matsunaga, who secretly uses the brainwaves of Marion Welch, a captured Zeon Newtype, to create a powerful but unstable combat AI. The system is installed in the RX-79BD-1 Blue Destiny Unit 1, a prototype mobile suit. Yuu Kajima is assigned to test the Blue Destiny, unaware of the system's origins. During a battle with Zeon forces, the EXAM System activates, granting the mobile suit extraordinary combat abilities but also triggering violent, uncontrollable behavior. Yuu struggles to maintain control over the machine while grappling with the ethical implications of using a human consciousness as a weapon.

The story explores the conflict between the Earth Federation and the Principality of Zeon, with both factions vying for control of the EXAM System. Zeon pilot Nimbus Schterzen, a rival to Yuu, becomes a central antagonist as he seeks to destroy the Blue Destiny and avenge the exploitation of Marion Welch. The narrative delves into themes of technological ethics, the horrors of war, and the psychological toll on soldiers and civilians alike.

As the series progresses, Yuu uncovers the truth about the EXAM System and Marion's tragic fate. He forms a bond with the system, which begins to exhibit traces of Marion's personality, further complicating his mission. The climax involves intense battles between the Blue Destiny and Zeon forces, culminating in a confrontation with Nimbus and the ultimate fate of the EXAM System. The story concludes with Yuu reflecting on the cost of war and the sacrifices made in the pursuit of technological advancement.

The manga provides a grounded perspective on the Gundam universe, focusing on the human element behind the machines and the moral dilemmas of warfare. It expands on the lore of the Universal Century while maintaining a tight, character-driven narrative.