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.
This Trojan is usually dropped on the affected systems by exploit kits.
Malwarebytes can remove Trojan.Bedep without further user interaction. You can expect to find more malware if this Trojan has been active.