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When designing the Delta Flyer in 2375, Tom Paris and Seven of Nine included photonic missiles in the vessel's armament. The missiles proved useful when combating the Malon, who were attempting to use their own shuttle to appropriate the USS Voyager's multispatial probe, which had become trapped in the atmosphere of a gas giant. (VOY: "Extreme Risk")
Later that year, Paris attempted to use a photonic missile to destroy an oxygen refinery under the surface of a large, spaceborne ocean, in an unauthorized attempt to stop the ocean's inhabitants, the Moneans, from damaging the containment field keeping the ocean intact. Before the missile could impact the refinery, however, it was intercepted and destroyed by a photon torpedo fired from Voyager. (VOY: "Thirty Days")