Why was Nicodemus killed?

Nicodemus was the most conscious, psychic, intelligent, magickal
being in the movie. With full use of his abilities, the rats and mice
of NIMH might have become immortal and surpassed even humans
in their evolution.

Why was Nicodemus killed off? And all of his magickal and
scientific apparatus, books, etc., lost?

Because we, the viewers -- the population -- are not supposed
to value consciousness and intelligence.

If we did, we might figure out who is controlling the world
and taking most of the value of what we produce, leaving only
1% of the wealth to be divided among 99% of the population.
We might identify who is at the top of the pyramid of control.

We might defeat them.

Instead, the film ends by telling us that _love_ is the most
important power. Romantic love, as illustrated by the two
crows. The subject of almost all the pop songs we're given
to fill our heads.

Psychedelics are banned for the same reason. People with
limited consciousness are easy to control, and easy to enslave
without their even realizing it.

Very safe and useful for the rulers.