The Output Window is an additional console that runs alongside Maya in Windows to give various diagnostic and status updates (specifically, stdout and stderr output). When performing certain calculation-heavy operations, Maya may send progress updates to the console instead of the main user interface. So if your interface appears to be frozen, check the Output Window to see if updates are being sent there instead.
The Output Window will open automatically when starting Maya on Windows. You can hide it by starting Maya via a command prompt along with the flag -hideConsole.
On Mac or Linux, you can view the console output directly in the terminal by starting Maya via /Applications/Autodesk/<maya version number>/Maya.app/Contents/MacOS/Maya on Mac or /usr/autodesk/<maya version number>/bin/maya.