A multi-partition Universal Serial Bus (USB) device has a flash memory with multiple partitions of storage. Some partitions are for different operating systems and store OS images. Another partition has a control program while a user partition stores user data and user configuration information. The control program can test the multi-partition USB device and instruct the host computer BIOS to mount a partition from its flash memory as a drive of the host computer. The host computer can then be rebooted. The OS image from the flash memory is loaded into main memory during rebooting, and the host computer executes a new operating system using the new OS image. The user can press buttons on the multi-partition USB device to select which OS to load, and to begin rebooting. Virus removal programs in the alternate OS can help recover from a virus in the primary OS.