"Buddy Complex: Into the Skies of Tomorrow" is a 13-episode anime series set in a futuristic world where humanity is divided by a global conflict. The story centers on Aoba Watase, a high school student who is unexpectedly thrust into the midst of a war between two powerful factions: the Free Pact Alliance and the Zogilia Republic. After being rescued by a mysterious pilot named Dio Weinberg, Aoba is recruited into the Free Pact Alliance and becomes a pilot of a humanoid weapon known as a Valiancer. His unique ability to synchronize with Dio, called the "Coupling System," makes him a valuable asset in the ongoing war.

The narrative explores the complexities of the conflict, revealing that the war is not merely a battle for territory but also involves time travel and alternate timelines. Aoba learns that his connection to Dio is rooted in events from the future, where the two were once close allies. As the story progresses, Aoba uncovers the truth behind his sudden involvement in the war and the role he plays in shaping the future. The series delves into themes of loyalty, friendship, and the consequences of altering time, as Aoba and his comrades navigate the challenges of their mission.

Key characters include Aoba Watase, whose journey from an ordinary teenager to a skilled pilot forms the emotional core of the story; Dio Weinberg, a skilled and enigmatic pilot with a deep connection to Aoba; and Hina Yumihara, a Zogilia pilot whose past and future are intertwined with Aoba's. The series balances intense mecha battles with character-driven drama, as the relationships between the pilots and their shared history drive the narrative forward. The story concludes with a resolution that ties together the threads of time travel and war, offering a satisfying conclusion to the central conflict.