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After Squad 13's failed attempt at a wedding, only the bride and groom are sent for re-indoctrination wiping out the relevant memories. But why stop there? Why didn't APE wipe the memory of every single member?

  • Everyone supported the wedding, and it probably served as a precedent to more relationships.
  • Obviously this makes the squad doubt Papa's benevolence, which compromises APE's plans.
  • Naturally everyone will try to restore the lost memories, which more or less works as they easily convince them that their relationship was real.

My only guess is that if they wipe everyone's memories they end up with a team full of strangers who won't perform as well as before, although that doesn't seem to be explicitly mentioned.

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In episode 18, APE sends the Nines to apprehend the bride and groom due to their forbidden knowledge.

Because Kokoro and Mitsuru are in a relationship and planning to have a wedding, as well as discussing forbidden knowledge about pregnancy, Papa orders the two to be re-indoctrinated

The reason why these two were the only ones taken to be re-indoctrinated was due to the events that took place in episode 17.

9'α holds up the childbirth handbook and asks if they recognize it. With Kokoro and Mitsuru's reaction, he says that they do. He asks for an explanation from Kokoro, since she's the one who dropped it. He says that it's strange, since it wouldn't have been provided in the study there, and it doesn't belong to her. Kokoro apologizes for not telling them all.
(emphasis my own)

While the rest of Squad 13 were involved in the wedding and planned a majority of it, it was the bride and groom who possessed the knowledge that APE considered dangerous.

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