"Mobile Suit Crossbone Gundam: Skull Heart" is a sequel to "Mobile Suit Crossbone Gundam," continuing the story of the Crossbone Vanguard and their fight against the oppressive Jupiter Empire. Set in the Universal Century timeline, the narrative takes place several years after the events of the original series. The protagonist, Tobia Arronax, returns as a central figure, now working as a teacher while secretly aiding the Crossbone Vanguard in their resistance efforts.

The story begins with the Jupiter Empire, led by the ruthless Crux Dogatie, attempting to expand its influence by deploying a new weapon called the "Angel Call." This device can manipulate Minovsky particles to disrupt communications and control mobile suits, posing a significant threat to Earth and its colonies. Tobia, alongside the Crossbone Vanguard, is drawn back into the conflict to counter this new menace. The group infiltrates the Jupiter Empire's forces, uncovering secrets about the Angel Call and its connection to the mysterious "Skull Heart," a powerful artifact with ties to the empire's ambitions.

Key characters include Tobia Arronax, whose experience and resolve make him a pivotal leader in the resistance; Bernadette Briett, a skilled pilot and ally; and Kincaid Nau, a former Crossbone Vanguard member with a complex past. The narrative explores themes of loyalty, sacrifice, and the consequences of technological advancement, as the characters navigate a war-torn universe filled with political intrigue and moral dilemmas.

The plot is driven by high-stakes battles, strategic maneuvers, and the personal struggles of the characters as they confront the Jupiter Empire's tyranny. The Crossbone Vanguard's efforts to protect humanity from the Angel Call and the Skull Heart form the core of the story, culminating in a climactic showdown that tests the limits of their resolve and ingenuity. The manga balances action-packed sequences with moments of introspection, providing a comprehensive exploration of its characters and their motivations within the larger Universal Century framework.