The most common and most likely answer to this crossword clue is the 9 letter word IMPERATOR
I've seen this crossword clue in The Guardian
I
M
P
E
R
A
T
O
R
More clues leading to the result IMPERATOR
Buddy explains!

The straight part
We know that "commander" is the straight/definition part of the clue. The straight part is often a synonym or definition, in this case commander = imperator.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 IMPERATOR mean?
IMPERATOR noun- An emperor.