Line a 13x9 pan with parchment paper and set aside.
In a large pan, bring water to a boil and cook pasta according to box directions.
While that is cooking, in a separate large pan, place squash and almond milk over medium heat and cook until squash is tender and can be mashed easily with a fork. About 10 min.
Add in the seasonings. Take off the heat and use an immersion blender to blend smooth. Add 6 oz of the cheese and turn the heat onto medium. Stir until well incorporated.
Drain the pasta and add to the cheese sauce, stir well, covering all the noodles. Pour into prepared pan, top with remaining cheese and bake 30 minutes, until golden brown.