Leave a mark on
'leave a mark on' is the definition.
(I've seen this in another clue)
This is all the clue.
(Other definitions for stain that I've seen before include "Blot" , "Black mark for saint" , "Penetrative dye; mark" , "Spot - shame" , "Blemish; colour (wood)" .)
(Other definitions for scar that I've seen before include "Steep cliff; skin mark" , "Bare rocky cliff - injury" , "Mark on body or tree" , "nine [AL CAPONE] had to face" , "fall could possibly be the reason for one" .)
(Other definitions for annotate that I've seen before include "Make notes upon" , "Supply explanatory notes" , "Add explanatory comments" , "Write down comments on" , "Mark" .)