The Master behind RLF is Theodore Eberbach from Schwarzesmarken
Copied from the Muv-Luv Alternative: Total Eclipse page: Something amusingly bad happened to him at the downfall of East Germany, and he became so disillusioned that he became a terrorist leader. See the following reasons:
They both have red hair.
The Dragon of RLF speaks German when piloting the SU47E.
The center of the map in his room has Berlin in its center.
They're both knife nuts
They are both voiced by Kenichi Suzumura, as per cast reveal for Schwarzesmarken.
Irisdina's death might be too painful for him to take, and he intends to take the world with him. Either that or he's actually trying to subvert or exploit Allegiance for his own ends.
Theodor's final words in the LN to Beatrix as he impales her with his combat knife were cut off from the anime, and goes 「……社会主義は、宗教を否定しているんじゃ無なかったのかよ」 (Communism is nothing, for it denies religion.). His flip-over may have started way earlier.
Related to the above: Katia will end up dying tragically after the events of Schwarzesmarken.
If Theodore really is the Master, than the death of Katia may be what finally pushes him over the edge.
She does die in one of the VN's alternate endings, which still provides Theodore enough drive to become the Master.
Beatrix was brainwashed into the Stasi
It's known from Requiem (specifically Gretel's sidestory) that Beatrix was a ruthless agent of the stasi by the time she was 18. Looking at her prequel arc so far, it seems increasingly unlikely that she'll willingly become the sadist she is in Schwarzesmarken. Beatrix was likely forced into the stasi sometime before the events of Jürgen's death due to some tragedy (maybe a political rival of her father's initiated a purge on the Brehmes). There, she was reprogrammed, much as Lise was so that when she reemerged, she was a completely changed person. It would explain the 180 in her personality and why she was willing to participate in the Moonlit Night purges of Alfred Strachwitz's (Jürgen's mentor and Katia's father) dissident faction in 1978, which would then lead to Beatrix having to purge Jürgen after Iris sold him out to save herself. This would explain Irisdina's and Beatrix's intense hatred of each other, as both blame the other for Jürgen's death.
Beatrix may have even been the one to force Iris into selling her out her brother. In the third chapter of SM's light novel, there doesn't seem to be much love left between Beatrix and Jürgen when she was thinking about him, and she may hate Irisdina as a psycho rival more than a vengeful lover.
Summaries from the latest Bernhard im Schatten chapter reveal that Beatrix's own father Abel forced her to enter the Stasi, and is attempting to break her moral compass by, for example, forcing her to kill runaways.
They have a same surname, and since Franz survived the the anime, it is possible that he might have escaped or emigrated to the West. It could be coincidence, but this theory could still hold some water.
It wouldn't be surprising given Anime logic, but Heim is a common Germanic last name, so any common ancestry they had probably split centuries ago.
