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It is possible to use a Thunderbolt Option ROM to circumvent the cryptographic signature checks in Apple's EFI firmware update routines. This allows an attacker with physical access to the machine to write untrusted code to the SPI flash ROM on the motherboard and creates a new class of firmware bootkits for the MacBook systems.
There are neither hardware nor software cryptographic checks at boot time of firmware validity, so once the malicious code has been flashed to the ROM, it controls the system from the very first instruction. It could use SMM and other techniques to hide from attempts to detect it.
Our proof of concept bootkit also replaces Apple's public RSA key in the ROM and prevents software attempts to replace it that are not signed by the attacker's private key. Since the boot ROM is independent of the operating system, reinstallation of OS X will not remove it. Nor does it depend on anything stored on the disk, so replacing the harddrive has no effect. A hardware in-system-programming device is the only way to restore the stock firmware.
Additionally, Thunderbolt devices' Option ROMs are writable from code that runs during the early boot and the bootkit could write copies of itself to new Thunderbolt devices. The devices remain functional, which would allow a stealthy bootkit to spread across air-gap security perimeters through shared Thunderbolt devices.
While the two year old Option ROM vulnerability that this attack uses can be closed with a few byte patch to the firmware, the larger issue of Apple's EFI firmware security and secure booting with no trusted hardware is more difficult to fix.