In the unzipped folder is a folder called mmd_tools. Copy the mmd_tools folder into Blender's scripts/add-ons folder. After opening Blender, click File, User Preferences. In User Preferences, Add-ons, ...

One of the most common errors that people make when installing a Blender add-on is failing to restart Blender. Also you cannot install mmd_tools directly from the .zip file.

At this time, iterations of Blender are available to download free for Windows, macOS, and Linux. This software can be downloaded from the official Blender website or Steam.