Cryptic crossword clue
Some thinker, supporter kept in check by government department 9

The most common and most likely answer to this crossword clue is the 9 letter word FOREBRAIN

I've seen this crossword clue in The Guardian
F
O
R
E
B
R
A
I
N

Buddy explains!

The straight part
We know that "Some thinker" is the straight/definition part of the clue. The straight part is often a synonym or definition, in this case some thinker = forebrain.
The cryptic/wordplay part
In cryptic crossword there's often an wordplay/cryptic part as well.
This part involves a more complex hint, such as an anagram, homophone, hidden word, etc.
Sadly, We don't have an explanation for this specific crossword clue yet.

What does FOREBRAIN mean?

FOREBRAIN noun
  1. The anterior part of the brain, including the cerebrum, thalamus, and hypothalamus.

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