Molecular dynamics computer simulations are employed to investigate processes leading to particle ejection from free-standing two-layered graphene irradiated by keV argon gas cluster projectiles. The effect of the primary kinetic energy and the projectile size on the ejection process is investigated. It has been found that both these parameters have a pronounced influence on the emission of particles. The interaction between argon projectiles and graphene is strong regardless of graphene's minimal thickness. A significant portion of the primary kinetic energy is deposited into the sample. Part of this energy is used for particle emission, which is substantial. As a result, circular nanopores of various dimensions are created depending on the bombardment conditions. A major part of the deposited energy is also dispersed in a form of acoustic waves. Different mechanisms leading to particle ejection and defect formation are identified depending on the projectile energy per atom. The implications of the results to a novel analytical approach in Secondary Ion Mass Spectrometry based on ultrathin free-standing graphene substrates and a transmission geometry are discussed.