Obfuscated Files or Information
Adversaries may attempt to make an executable or file difficult to discover or analyze by encrypting, encoding, or otherwise obfuscating its contents on the system or in transit. This is common behavior that can be used across different platforms and the network to evade defenses.
Portions of files can also be encoded to hide the plain-text strings that would otherwise help defenders with discovery.  Payloads may also be split into separate, seemingly benign files that only reveal malicious functionality when reassembled. 
Adversaries may also obfuscate commands executed from payloads or directly via a Command-Line Interface. Environment variables, aliases, characters, and other platform/language specific semantics can be used to evade signature based detections and whitelisting mechanisms.   
Another example of obfuscation is through the use of steganography, a technique of hiding messages or code in images, audio tracks, video clips, or text files. One of the first known and reported adversaries that used steganography activity surrounding Invoke-PSImage. The Duqu malware encrypted the gathered information from a victim's system and hid it into an image followed by exfiltrating the image to a C2 server.  By the end of 2017, an adversary group used Invoke-PSImage to hide PowerShell commands in an image file (png) and execute the code on a victim's system. In this particular case the PowerShell code downloaded another obfuscated script to gather intelligence from the victim's machine and communicate it back to the adversary. 
Most of the strings in ADVSTORESHELL are encrypted with an XOR-based algorithm; some strings are also encrypted with 3DES and reversed. API function names are also reversed, presumably to avoid detection in memory.
FinFisher is heavily obfuscated in many ways, including through the use of spaghetti code in its functions in an effort to confuse disassembly programs. It also uses a custom XOR algorithm to obfuscate code.
Some strings in are obfuscated with XOR x56.
Kazuar is obfuscated using the open source ConfuserEx protector. Kazuar also obfuscates the name of created files/folders/mutexes and encrypts debug messages written to log files using the Rijndael cipher.
OopsIE uses the Confuser protector to obfuscate an embedded .Net Framework assembly used for C2. OopsIE also encodes collected data in hexadecimal format before writing to files on disk and obfuscates strings.
Pisloader obfuscates files by splitting strings into smaller sub-strings and including "garbage" strings that are never used. The malware also uses return-oriented programming (ROP) technique and single-byte XOR to obfuscate data.
Ensure logging and detection mechanisms analyze commands after being processed/interpreted, rather than the raw input. Consider utilizing the Antimalware Scan Interface (AMSI) on Windows 10 for this functionality. 
Mitigation of compressed and encrypted files sent over the network and through email may not be advised since it may impact normal operations.
Detection of file obfuscation is difficult unless artifacts are left behind by the obfuscation process that are uniquely detectable with a signature. If detection of the obfuscation itself is not possible, it may be possible to detect the malicious activity that caused the obfuscated file (for example, the method that was used to write, read, or modify the file on the file system).
Flag and analyze commands containing indicators of obfuscation and known suspicious syntax such as uninterpreted escape characters like '''^''' and '''"'''. Windows' Sysmon and Event ID 4688 displays command-line arguments for processes. Deobfuscation tools can be used to detect these indicators in files/payloads.   
Obfuscation used in payloads for Initial Access can be detected at the network. Use network intrusion detection systems and email gateway filtering to identify compressed and encrypted attachments and scripts. Some email attachment detonation systems can open compressed and encrypted attachments. Payloads delivered over an encrypted connection from a website require encrypted network traffic inspection.
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