A method, system, and computer program product for protecting a computer system provides bootstrap operating system detection and recovery and provides the capability to detect malware, such as rootkits, before the operating system has been loaded and provides the capability to patch malfunctions that block the ability of the computer system to access the Internet. A method for protecting a computer system includes reading stored status information indicating whether network connectivity was available the last time an operating system of the computer system was operational, when the stored status information indicates that network connectivity was not available, obtaining a software patch, and executing and applying the software patch.