What does the cryptic crossword clue "Stone deepest of all, also in empty box (4)" mean?

The definition is "Stone". The wordplay uses acrostic. last letters of "also in empty box" = ONYX; definition: "Stone" The answer is ONYX.

Stone deepest of all, also in empty box (4)

Guardian Cryptic #29460 | 23 Down | 2024-08-13 flower