Custom Command and Control Protocol
Adversaries may communicate using a custom command and control protocol instead of encapsulating commands/data in an existing Standard Application Layer Protocol. Implementations include mimicking well-known protocols or developing custom protocols (including raw sockets) on top of fundamental protocols provided by TCP/IP/another standard network stack.
APT32 uses Cobalt Strike's malleable C2 functionality to blend in with network traffic. The group's backdoor can also exfiltrate data by encoding it in the subdomain field of DNS packets. Additionally, one of the group's macOS backdoors implements a specific format for the C2 packet involving random values.
Cobalt Strike allows adversaries to modify the way the "beacon" payload communicates. This is called "Malleable C2" in the Cobalt Strike manual and is intended to allow a penetration test team to mimic known APT C2 methods.
Duqu is capable of using its command and control protocol over port 443. However, Duqu is also capable of encapsulating its command protocol over standard application layer protocols. The Duqu command and control protocol implements many of the same features as TCP and is a reliable transport protocol.
If NETEAGLE does not detect a proxy configured on the infected machine, it will send beacons via UDP/6000. Also, after retrieving a C2 IP address and Port Number, NETEAGLE will initiate a TCP connection to this socket. The ensuing connection is a plaintext C2 channel in which commands are specified by DWORDs.
PLATINUM has used the Intel® Active Management Technology (AMT) Serial-over-LAN (SOL) channel for command and control.
UBoatRAT has used a custom command and control protocol to communicate with C2. The string ‘488’ is placed at the top of the payload and encrypts the entre buffer with a static key using a simple XOR cipher.
Properly configure firewalls and proxies to limit outgoing traffic to only necessary ports and through proper network gateway systems. Also ensure hosts are only provisioned to communicate over authorized interfaces.
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 may be based on the specific protocol used by a particular adversary or tool, and will likely be different across various malware families and versions. Adversaries will likely change tool C2 signatures over time or construct protocols in such a way as to avoid detection by common defensive tools. 
Analyze network traffic for ICMP messages or other protocols that contain abnormal data or are not normally seen within or exiting the network.
Analyze network data for uncommon data flows (e.g., a client sending significantly more data than it receives from a server). Processes utilizing the network that do not normally have network communication or have never been seen before are suspicious. Analyze packet contents to detect communications that do not follow the expected protocol behavior for the port that is being used. 
Monitor and investigate API calls to functions associated with enabling and/or utilizing alternative communication channels.
- Carr, N.. (2017, May 14). Cyber Espionage is Alive and Well: APT32 and the Threat to Global Corporations. Retrieved June 18, 2017.
- Mudge, R. (2014, July 14). Github Malleable-C2-Profiles safebrowsing.profile. Retrieved June 18, 2017.
- Dahan, A. (2017). Operation Cobalt Kitty. Retrieved December 27, 2018.
- Dumont, R. (2019, March 20). Fake or Fake: Keeping up with OceanLotus decoys. Retrieved April 1, 2019.
- Dumont, R.. (2019, April 9). OceanLotus: macOS malware update. Retrieved April 15, 2019.
- FireEye. (2018, February 20). APT37 (Reaper): The Overlooked North Korean Actor. Retrieved March 1, 2018.
- Mandiant. (n.d.). Appendix C (Digital) - The Malware Arsenal. Retrieved July 18, 2016.
- Bennett, J., Vengerik, B. (2017, June 12). Behind the CARBANAK Backdoor. Retrieved June 11, 2018.
- Sebastian Feldmann. (2018, February 14). Chaos: a Stolen Backdoor Rising Again. Retrieved March 5, 2018.
- Strategic Cyber LLC. (2017, March 14). Cobalt Strike Manual. Retrieved May 24, 2017.
- Huss, D.. (2016, March 1). Operation Transparent Tribe. Retrieved June 8, 2016.
- Ash, B., et al. (2018, June 26). RANCOR: Targeted Attacks in South East Asia Using PLAINTEE and DDKONG Malware Families. Retrieved July 2, 2018.
- Fidelis Cybersecurity. (2016, February 29). The Turbo Campaign, Featuring Derusbi for 64-bit Linux. Retrieved March 2, 2016.
- Windows Defender Advanced Threat Hunting Team. (2016, April 29). PLATINUM: Targeted attacks in South and Southeast Asia. Retrieved February 15, 2018.
- Symantec Security Response. (2011, November). W32.Duqu: The precursor to the next Stuxnet. Retrieved September 17, 2015.
- Brandt, A.. (2019, May 5). Emotet 101, stage 4: command and control. Retrieved April 16, 2019.
- Manea, D.. (2019, May 25). Emotet v4 Analysis. Retrieved April 16, 2019.
- Hromcová, Z. (2018, June 07). InvisiMole: Surprisingly equipped spyware, undercover since 2013. Retrieved July 10, 2018.
- Gross, J. (2016, February 23). Operation Dust Storm. Retrieved September 19, 2017.
- Miller-Osborn, J. and Grunzweig, J.. (2017, March 30). Trochilus and New MoonWind RATs Used In Attack Against Thai Organizations. Retrieved March 30, 2017.
- Neville, A. (2012, June 15). Trojan.Naid. Retrieved February 22, 2018.
- Symantec Security Response. (2012, June 18). CVE-2012-1875 Exploited in the Wild - Part 1 (Trojan.Naid). Retrieved February 22, 2018.
- FireEye Labs. (2015, April). APT30 AND THE MECHANICS OF A LONG-RUNNING CYBER ESPIONAGE OPERATION. Retrieved May 1, 2015.
- Unit 42. (2017, December 15). Unit 42 Playbook Viewer. Retrieved December 20, 2017.
- Dell SecureWorks Counter Threat Unit Threat Intelligence. (2015, August 5). Threat Group-3390 Targets Organizations for Cyberespionage. Retrieved August 18, 2018.
- Grunzweig, J. and Miller-Osborn, J. (2017, November 10). New Malware with Ties to SunOrcal Discovered. Retrieved November 16, 2017.
- FireEye iSIGHT Intelligence. (2017, April 6). APT10 (MenuPass Group): New Tools, Global Campaign Latest Manifestation of Longstanding Threat. Retrieved June 29, 2017.
- Kaspersky Lab's Global Research and Analysis Team. (2014, November 24). THE REGIN PLATFORM NATION-STATE OWNAGE OF GSM NETWORKS. Retrieved December 1, 2014.
- Symantec Security Response. (2016, August 8). Backdoor.Remsec indicators of compromise. Retrieved August 17, 2016.
- Kaspersky Lab's Global Research & Analysis Team. (2016, August 9). The ProjectSauron APT. Retrieved August 17, 2016.
- Falcone, R., et al. (2018, July 27). New Threat Actor Group DarkHydrus Targets Middle East Government. Retrieved August 2, 2018.
- Lee, B., Falcone, R. (2019, January 18). DarkHydrus delivers new Trojan that can use Google Drive for C2 communications. Retrieved April 17, 2019.
- Faou, M. and Boutin, J.. (2017, February). Read The Manual: A Guide to the RTM Banking Trojan. Retrieved March 9, 2017.
- US-CERT. (2018, June 14). MAR-10135536-12 – North Korean Trojan: TYPEFRAME. Retrieved July 13, 2018.
- Hayashi, K. (2017, November 28). UBoatRAT Navigates East Asia. Retrieved January 12, 2018.
- US-CERT. (2017, November 22). Alert (TA17-318B): HIDDEN COBRA – North Korean Trojan: Volgmer. Retrieved December 7, 2017.
- US-CERT. (2017, November 01). Malware Analysis Report (MAR) - 10135536-D. Retrieved July 16, 2018.
- Lee, B., Falcone, R. (2018, June 06). Sofacy Group’s Parallel Attacks. Retrieved June 18, 2018.
- Gardiner, J., Cova, M., Nagaraja, S. (2014, February). Command & Control Understanding, Denying and Detecting. Retrieved April 20, 2016.