What happened to Maria and Mamoru?
Although it was not explicitly stated in the Anime. The following sequence of events was strongly implied and was part of Squealer's master plan.


Squealer helps Maria and Mamoru escape. Furthermore, he lets them stay and live with the colony.
Squealer waits for (or sweet-talks) Maria and Mamoru into having a child.
Once the child is born, Squealer (and/or his fellow rats) kills Maria and Mamoru.
They take the child and raise him/her. ("him" in the Novel, "her" in the Anime)
Squealer then takes the bones of Maria and Mamoru and gives them to the ethics committee.


When Squealer says that he will prepare fake remains for the villagers to find and that it will "take some time". He really means the actual remains of Maria and Mamoru and that it will "take some time" for them to have a child.



The sole purpose of this was to get a human child that could be raised into an Akki* and used against humans in Squealer's pursuit of world domination.

*I use Akki for short. But they really aren't. In reality, the children raised by the rats will believe themselves to be rats, thus attack inhibition and death-feedback will apply to rats instead of humans.