Stopping the assessment and informing the emergency contact is the best thing to do next after identifying that an application being tested has already been compromised with malware. This is because continuing the assessment might interfere with an ongoing investigation or compromise evidence collection. The emergency contact is the person designated by the client who should be notified in case of any critical issues or incidents during the penetration testing engagement.
Reference: https://www.redteamsecure.com/blog/my-company-was-hacked-now-what