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Their duty is to monitor any alien activity happening on Earth. They seem to treat every alien as a threat and mistakenly identify Timmy as an alien since he has no records on Earth and are not interested in any type of dialouge or peacful exchange. Instead they capture and demand Timmy to surrender so they can dissect him but Timmy manages to distract them and escapes. They later appear ignoring Timmy's warnings about attacking the Eliminator which would prove to be a mistake as the Eliminator absorbed their weapons and made them his minions. After the Eliminator and Darkness both are defeated, it is most likely the MERF Agents were returned to normal and returned to theri normal jobs.