Truly Amazing Mac and Cheese

2 Tbs. unsalted butter 

1/4 cup all-purpose flour 

3 cups milk 

1 small yellow onion, thinly sliced 

1/2 bay leaf 

Pinch of grated nutmeg 

Kosher salt and freshly ground pepper, to taste 

1/2 lb. macaroni shells or other shape 

2 Tbs. unsalted butter 

1 1/2 cups mixed grated hard cheeses such as aged cheddar, Gruyère and Parmigiano-Reggiano 

1/2 cup heavy cream 

Kosher salt and freshly ground pepper, to taste