Adversaries may use more than one remote access tool with varying command and control protocols as a hedge against detection. If one type of tool is detected and blocked or removed as a response but the organization did not gain a full understanding of the adversary's tools and access, then the adversary will be able to retain access to the network. Adversaries may also attempt to gain access to Valid Accounts to use External Remote Services such as external VPNs as a way to maintain access despite interruptions to remote access tools deployed within a target network. 
Use of a Web Shell is one such way to maintain access to a network through an externally accessible Web server.
3PARA RAT will sleep until after a date/time value loaded from a .dat file has passed. This allows the RAT to remain dormant until a set date, which could allow a means to regain access if other parts of the actors' toolset are removed from a victim.
OilRig has used RGDoor via Web shell to establish redundant access. The group has also used harvested credentials to gain access to Internet-accessible resources such as Outlook Web Access, which could be used for redundant access.
Identify and block potentially malicious software that may be used as a remote access tool, and audit and/or block it by using whitelisting  tools, like AppLocker,   or Software Restriction Policies  where appropriate. 
Network intrusion detection and prevention systems that use network signatures to identify traffic for specific adversary malware can be used to mitigate activity at the network level. Signatures are often for unique indicators within protocols and will be different across various malware families and versions. Adversaries will likely change tool signatures over time or construct protocols in such a way as to avoid detection by common defensive tools. 
Existing methods of detecting remote access tools are helpful. Backup remote access tools or other access points may not have established command and control channels open during an intrusion, so the volume of data transferred may not be as high as the primary channel unless access is lost.
Detection of tools based on beacon traffic, Command and Control protocol, or adversary infrastructure require prior threat intelligence on tools, IP addresses, and/or domains the adversary may use, along with the ability to detect use at the network boundary. Prior knowledge of indicators of compromise may also help detect adversary tools at the endpoint if tools are available to scan for those indicators.
If an intrusion is in progress and sufficient endpoint data or decoded command and control traffic is collected, then defenders will likely be able to detect additional tools dropped as the adversary is conducting the operation.
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