Innermost means nearest the very middle. The last layer in, with nothing further to go.
The physical sense is straightforward, as in the innermost chamber of a tomb or the innermost ring of a tree. The figurative one is far commoner and always about secrecy: innermost thoughts, innermost feelings, innermost fears. Those are the things kept furthest from anybody else, and the word is nearly always plural in that use. Its opposite is outermost, which does the same job in reverse and is used far less.
Old English
innemest — innermost
Middle English
innermost
English, today
innermost
Built from
From Middle English innermost, innermest, in-nermast, alteration (due to Middle English inner, innere (“inner”)) of Old English innemest (“innermost”), equivalent to inner + most.
Etymology from Wiktionary, CC BY-SA