Story with a lesson about a Tom hiding his head is comprehensible (10)
'comprehensible' is the definition.
(associated in meaning)
'story with a lesson about a tom hiding his head' is the wordplay.
'story with a lesson' becomes 'fable'.
'about' is an insertion indicator.
'hiding' means one lot of letters goes inside another.
'head' suggests taking the first letters.
The first letter of 'his' is 'h'.
'fable' placed around 'atom' is 'fatomable'.
'fatomable' going around 'h' is 'FATHOMABLE'.
'is' acts as a link.
(Other definitions for fathomable that I've seen before include "Comprehensible", "understandable".)