Trojan.Agent refers to a generic Trojan malware detection. It is used for detections that are either associated with no specific malware families or not enough information is available to pinpoint the malware family.
Trojan.Fileless.MTGen is a generic detection for the startup locations in use by fileless infections that gain persistence by creating registry keys on Windows systems.
More information about fileless infections can be found in our blog post, Fileless Infections: An Overview.
In the majority of the cases, the registry keys created by Trojan.Fileless.MTGen are designed to run Powershell commands that carry out the rest of the infection. Other than Powershell, we have also seen the mshta command used as such.
Malwarebytes protects users from Trojan.Fileless.MTGen by using real-time protection to block the trojans that create them.
Malwarebytes can detect and remove Trojan.Fileless.MTGen without further user interaction.