You missed the carbon atoms, and specifically the carbon atoms in the central ring which are bonded to nitrogen and sulfur. When the methylene blue is in its reduced leuco state, each of these has one bond to the more electronegative atoms and none to hydrogen (the only other element in the molecule), thus you count out the oxidation state as +1 for all four of these carbons.
Now you shake the bottle and it turns blue. Note that in this form two of the central carbons now have two bonds to the nitrogen or sulfur, so they have been oxidized from +1 to +2. Which two carbons get oxidized depends on which of multiple contributing structures you draw, but the net result is always you oxidize two carbon atoms by one unit.
Half the available contributing structures have the two carbon atoms on the left side of the central ring oxidized, and half have the carbon atoms on the right half oxidized. Since the two halves are equivalent, if you are into fractional oxidation numbers you can say that "on average" the four central carbon atoms each go from +1 to +1.5.