"Schwarzesmarken" is a 12-episode anime series set in an alternate 1983, where humanity is engaged in a prolonged war against alien beings known as BETA. The story unfolds in East Germany, a nation under the oppressive control of the Stasi, the state security service. The series centers on the 666th TSF Squadron, also called "Schwarzesmarken," an elite unit of Tactical Surface Fighters (TSFs), piloted by soldiers tasked with defending humanity against the BETA threat.

The protagonist, Theodor Eberbach, is a skilled TSF pilot and a member of the 666th Squadron. Theodor harbors deep resentment toward the Stasi due to their brutal methods and the personal trauma they inflicted on his family. His sister, Lise, was subjected to inhumane experiments by the Stasi, leaving her physically and mentally scarred. Theodor's primary motivation is to protect his sister and seek justice against those responsible for her suffering.

The 666th Squadron is led by Irisdina Bernhard, a calm and composed commander who balances her loyalty to East Germany with her moral convictions. Her younger sister, Katia Waldheim, serves as the squadron's political officer, representing the Stasi's interests within the unit. Katia's idealism and naivety often clash with the harsh realities of war and the Stasi's oppressive tactics. The squadron also includes Gretel Jeckeln, a pragmatic and skilled pilot, and Beatrix Brehme, a former Stasi operative with a mysterious past.

As the series progresses, the 666th Squadron faces escalating threats from both the BETA and internal political strife. The Stasi's manipulation and surveillance create tension within the unit, while the BETA's relentless attacks push the pilots to their limits. Key events include a failed mission to rescue a high-ranking official, the revelation of a covert Stasi operation to develop advanced BETA-based weapons, and a climactic battle against a massive BETA hive.

The narrative explores themes of loyalty, betrayal, and the moral complexities of war. Characters are forced to confront their beliefs and make difficult choices, often at great personal cost. The series concludes with a decisive confrontation between the 666th Squadron and the Stasi, as Theodor and his comrades strive to protect their ideals and secure a future free from oppression. The ending leaves some questions unresolved, reflecting the ongoing struggle against both external and internal threats.