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Heat oven to 180C/160C fan/gas 4. Toss two-thirds of the butternut squash with the olive oil and seasoning, and roast for 20 mins until nearly tender (it will finish cooking later). Chop the remaining squash coarsely, put in a heatproof bowl with 100ml water and cover with cling film. Microwave on High for 8-10 mins until tender. Drain and mash.
Fry the onion in a knob of butter until softened but not browned, about 5 mins. Stir in the chopped sage and cook for 1 min more, then add the remaining butter to melt. Stir in the flour and mustard powder, and cook for 1 min until it forms a paste. Gradually whisk in splashes of milk (you can add in bigger additions as you go) until you have a smooth sauce. Bubble, stirring constantly, for 3-5 mins until thickened. Take off the heat and whisk in the mashed squash, 200g of the cheddar and half the Parmesan. Season to taste.
Cook the macaroni following pack instructions. Drain well, then stir into the sauce with the roasted squash. Tip into a baking dish and scatter with the remaining cheese and sage leaves. Can be made up to a day ahead at this point – cool and keep in the fridge. If freezing, don’t add the whole sage leaves.
Heat oven to 180C/160C fan/gas 4 again. Splash the sage leaves with oil and bake for 40 mins until bubbling and golden on top.