Heat the oil over a medium high heat in a large saucepan or Dutch oven. Once it is shimmering, add the onion with a generous pinch of salt and cook for 10 minutes, or until soft and slightly golden.
Add the sausage, breaking it up with the back of your spoon. Cook until browned.Stir in the crushed garlic and red pepper flakes, cooking for a further few minutes until the garlic is aromatic.
Stir in the marinara sauce, scraping any browned bits off the bottom of the pot. Reduce the heat to medium low, season well with black pepper, and allow to simmer for 20 minutes.
Stir in the milk and the lemon zest, and simmer for a further 10 minutes.
Meanwhile, preheat the oven to 400F and cook the pasta shells as per the packets instructions in a pan of boiling, salted water. You want them to be just tender, but still with a good amount of bite. Drain and set aside.
Check to see if you want to add any more salt or pepper to the sauce before assembling the shells.
Spoon a generous amount of the sauce into the bottom of a large oven dish or shallow casserole. Then, to assemble the shells, spoon a little creme fraiche into each one, topping up with sauce, then nestling join side up in the pan.
Spoon over any remaining sauce, and scatter over the shredded cheese.
Bake for 20-25 minutes until the sauce is bubbling, and the cheese is melty and golden.
Rest for 5 minutes before sprinkling over the shredded basil and serving.