What is a "splinter cell" exactely?

Uhh as far as this franchise goes, it has something to do with being invisible and deadly like a shard of glass or something like that.

A Splinter Cell is a covert operations field agent. They are charged with performing whatever actions necessary to promote the public good of the U.S.
In other words...it's just Ubisoft's made up title for a spy/secret agent whatever.