MySQL Internals: SQL Execution Flow
There isn't a clear-cut flow chart online for this, but if you want to understand how it all comes together for InnoDB, one of the best explanations I have seen are at M18 Deep Dive InnoDB Transactions and Write Paths. The slideshow is available at https://mariadb.org/wp-content/uploads/2018/07/Deep-Dive_-InnoDB-Transactions-and-Write-Paths.pdf

That presentation is for MariaDB, but MySQL should be quite similar.

The presentation of overall architecture of MySQL 8.0 at https://www.percona.com/resources/webinars/mysql-80-architecture-and-enhancement is also quite clear.