How do I call Matlab code into Simulink for doing a simulation for doing plots?

There's a Matlab function block. Follow the example and your inputs and outputs will create source/sink connections on the Simulink block to wire in values.

I would only put the controller in there, and don't use the clear all command - if it's not persistent then a variable inside a function ceases to exist between function calls. Every call to the function wipes all the internal variables inside that function.

If you're wanting your data to be plotted at the end then you can use a To Workspace block and send the data out that way and plot from the console or script after the Simulink project finishes.