"Muv-Luv Alternative: Total Eclipse" is set in an alternate timeline where humanity faces extinction due to an alien species known as BETA (Beings of Extra Terrestrial origin which are Adversary of humanity). The story unfolds in the late 20th century, where Earth is under siege by these extraterrestrial invaders. To combat the BETA, humanity develops Tactical Surface Fighters (TSFs), humanoid mechs piloted by skilled soldiers. The narrative primarily centers on the development and testing of advanced TSF technology, as well as the personal and political conflicts among the international teams involved.

The protagonist, Yūya Bridges, is a Japanese-American TSF pilot and test pilot for the United Nations. He is assigned to the Yukon Base in Alaska, where he joins an international team tasked with developing the next generation of TSFs. Yūya is initially portrayed as a lone wolf, driven by personal loss and a desire for revenge against the BETA. His aloof demeanor and reluctance to cooperate with others create tension within the team.

The story introduces several key characters, including Cryska Barchenowa and Inia Sestina, two young Soviet pilots who are part of a secretive experimental program. They pilot advanced TSFs known as the Su-37UB Terminator and Su-37UM2 Schwarzesmarken, respectively. Their presence adds complexity to the narrative, as their mysterious backgrounds and unique abilities raise questions about the ethics of their development and deployment.

As the team conducts tests and missions, interpersonal conflicts and rivalries emerge, particularly between Yūya and other pilots. The series explores themes of loyalty, sacrifice, and the moral dilemmas of warfare, as the characters grapple with their roles in the fight against the BETA. Political intrigue also plays a significant role, as various nations vie for control over the new TSF technology, often prioritizing their own interests over global unity.

The narrative builds toward a climactic confrontation with the BETA, during which the team must overcome their differences and work together to survive. The series balances intense mecha combat with character-driven drama, highlighting the human cost of war and the resilience of those who fight on the front lines. Through its exploration of both personal and global stakes, "Muv-Luv Alternative: Total Eclipse" presents a multifaceted portrayal of humanity's struggle for survival in the face of overwhelming odds.