Graphene is a fascinating 2D material that is being widely investigated for use in electronic devices due to its unique electronic and material properties. Also, because of its high thermal stability and inertness, it is considered a promising candidate for use as a protection layer for metal substrates. Here, the reaction of oxygen (O\(_2\)) with graphene films grown on Ru(0001) is investigated with helium low energy ion scattering (LEIS). LEIS spectra collected at different scattering angles confirm that oxygen does not adsorb to graphene, but instead intercalates between the graphene and the substrate. The intercalated O\(_2\) desorbs when the sample is annealed to 800 K. Since this is a much lower temperature than is needed to remove atomic oxygen adatoms chemisorbed onto Ru, it is inferred that the intercalated oxygen is molecular. During the desorption process, some of the graphene is etched away due to a chemical reaction with the oxygen, with the proportion desorbing as O\(_2\) or reacting to etch the graphene being dependent on the amount of intercalated O\(_2\).