What Is The Best Method/Tool To Investigate WordPress Internal Performance?

You should look at the queries there run on the pages, with and without plugins and custom Theme. So you have the possibility to compare the process and find the bottlenecks.
As helping tools should I named:

Activate the debug mode so that you also get errors and the usage of minified scripts and deactivation of caching. Helpful page is https://wordpress.org/support/article/debugging-in-wordpress/

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