The Intel Microcode Boot Loader creates a bootable USB flash drive that automatically applies the latest Intel microcodes to your identified CPU so that you are protected from the speculative execution side-channel attacks called Spectre.
Spectre is vulnerability found in Intel & AMD CPUs that allow a malicious process to steal information from another running process on the computer. To fix these vulnerabilities, Intel released updated microcodes that patch Intel CPUs so that they become protected from the vulnerability.
For Windows 10 and Windows Server 2016 users, Microsoft distributed these updated microcodes automatically as a Windows update. Unfortunately, older operating systems and thus the CPUs that run them, would not be receiving the patches and would not be protected. This is where the Intel Microcode Boot Loader comes into play.