Preheat crockpot to high.
In a medium skillet, heat olive oil over medium heat. Stir in onion and garlic and cook until softened and fragrant, about 3 minutes. Add thyme and cook 2-3 minutes.
Add to warmed crockpot along with the bay leaves, broth, plus the squash and dry lentils. Stir, cover and cook in crockpot for 3-4 hours on high or until squash is very tender.
Meanwhile, cook pasta according to package directions to make them al dente.
Once the squash is cooked, remove bay leaves from mixture. Using an immersion blender, puree the squash to create a smooth sauce (you can place in a regular blender if you don't own an immersion blender).
Stir in milk and cheese. Taste and adjust seasoning and cheese to your liking. Sauce should be slightly sweet due to the addition of the squash.
Toss with cooked pasta and serve with extra cheese, add in optional veggies or top with a pinch of red pepper flakes or hot sauce, if desired.