An East German TSF squadron, the 666th or "Schwarzesmarken", enter the fight against the BETA with their Comrade Captain, Irisdina Bernhard. Pilot Anett Hosenfield suffers a nervous breakdown and, in the chaos it creates, pilot Inghild Bronikowski is mortally wounded. Irisdina administers a coup de grace rather than leave Inghild to die on the battlefield. She castigates Second Lieutenant Theodor Eberbach for failing to help Annett, and assigns him to continue the mission while Inghild's body is recovered.

After finishing training for laserjagd, the squadron's technique for hunting Laser-class BETA, the Stasi arrive. They demand to take Katia to clarify some things because she is from the West and was admitted to the 666th with unusual haste. Heinz Axmann, of the Stasi, also states that the rumors about Irisdina are true, adds that she will someday kill her squadron, and tells Katia that they will see her soon.

Katia and the injured Pham are brought inside the besieged Fort Neuenhagen. Back at Bebersee Base, Gretel asks Theodor if he and Irisdina are plotting something. She reveals that five years earlier, a coup against the Stasi led by General Strachwitz was foiled, and the Stasi effectively erased him from history. Gretel also tells Theodor the story of Irisdina selling out her brother to the Stasi is almost certainly a lie. Armed with this information, Theodor arranges a meeting with Irisdina in an old church, where she admits her "dog of the Stasi" persona is a cover, and she's plotting to overthrow the Stasi herself, and recruits Theodor into her cause.

Irisdina introduces Lise to the squadron, to the shock of Theodor, who cannot believe he's been reunited with his sister after being separated three years ago. Irisdina and Gretel express concern Lise may have been brainwashed, sent as a spy against the National People's Army and the 666th specifically. Irisdina orders Theodor to figure out what Lise is up to. During a training exercise, they meet up with European Union forces, and join an operation to retake BETA-held territory in the former Poland with the goal of expanding a beachhead near Gdańsk.

In the recaptured Gdańsk base, West Germain Huckebein battalion leader Circe Steinhoff berates the Schwarzesmarken for needing to be rescued. She gets into a fistfight with Annett, which is broken up by Katia. Irisdina reveals to Theodor and Katia that the whole reason for the joint mission is to improve the military's stature relative to the Stasi, which explains Gretel's obsession with appearances. Facing a second wave of 40,000 BETA, the Warsaw Pact forces plan a response that will put the 666th in the greatest danger, but will also prove their mettle compared to the EU and US' conservative tactics.

Back at base, Gretel and Irisdina grill Theodor about Lise's loyalties, and he asserts that she's loyal to him and not a Stasi plant. They also reveal that with the activation of a BETA hive in Minsk, East Germany will soon be overwhelmed with a new BETA assault. Along with all of this, the Stasi is on the verge of taking over the military, having arrested many NPA officials. Axmann arrives with a TSF squadron, briefly arresting Irisdina for "counterrevolutionary statements" during the earlier battle, and accusing Lise of being a Stasi spy.

The BETA assault from Minsk is worse than expected, with 200,000 BETA headed towards Fort Seelow, where the army will make its final stand to protect Berlin. With doubts about Lise growing in the squad, Theodor asserts her innocence to Irisdina, and acknowledges he has begun a sexual relationship with Lise, his adoptive sister, in order to keep an eye on her. The BETA overwhelm artillery forces with the Heavy Laser-class, and the 666th is sent to engage them.

Theodor and Katia escape the base, leaving the rest of the squad captured by Lise. In Berlin, where the Moscow faction of the Stasi has beaten Axmann's Berlin faction, Schmidt takes control of the government, vowing to unite all military forces under the Stasi. Beatrix arrives at Bebersee, where she re-inducts Lise to the Stasi's Werewolf battalion, and orders Lise to interrogate the captured members of the 666th. Katia and the dejected Theodor escape into the woods, where they are rescued by Gretel, who is now working with a resistance organization.

General Heim accepts Katia as a figurehead of the resistance and plans an attack on the Stasi in Berlin. At Bebersee Base, Lise oversees the interrogation of the captured members of the 666th. Theodor and Gretel lead the rebels in an attack on Bebersee to free the captured members.

The West German government takes note of the Stasi coup d'etat and is prepared to recognize them as the new government, only so that the East will hold the line against the BETA. Circe heads to the east to rendezvous with the rebels, hoping to bring back some proof they can win. Lise, now embedded with Borkewald squadron, attacks the leaked location of a rebel leadership meeting in Neuruppin.

Attempting to return to Berlin, the 666th and their resistance allies are met by Werewolf Squadron at the Havel River. Gretel is shot down, but is found by Axmann, who invites her to join his Berlin faction in the internal Stasi rivalry against the Moscow faction.

The rebels take over Berlin's broadcast tower and escort Katia inside. The 666th and the rebels engage Werewolf squadron over the streets of Berlin. During the battle, they hear Katia's speech, revealing herself to the nation as Usula Strachwitz, and appealing for the people to rise up against the Stasi.