Preheat the oven to 425° F.
Heat a large dutch oven or high sided skillet over medium high heat. Add 2 tbsp olive oil. When shimmering, add the squash and cook for 5-7 minutes, gently stirring once or twice, until just beginning to brown. Transfer the squash to a plate and set aside.
Reduce the heat slightly and add the remaining 1 tbsp of olive oil to the pot along with the onion. Sauté until translucent, about 3-4 minutes. Add the thyme, nutmeg, balsamic vinegar and rice. Toast, stirring frequently, for 5 minutes or until fragrant. Stir in the chickpeas and season generously with salt and pepper.
Transfer the contents of the pot to a large rectangular baking dish (about 8”x12”) and mix in the squash. Pour over the boiling water and cover tightly with foil. Bake for 30 minutes then let sit for 10 minutes before removing the foil and fluffing.
To make the sage pesto, heat a skillet over medium heat. Add the pumpkin seeds and toast for 5-7 minutes, tossing occasionally, until golden brown and popping.
Add the seeds to the bowl of a food processor along with the remaining ingredients. Pulse until smooth, adding water, 1 tbsp at a time until a desired consistency is reached. Taste for salt and adjust as needed.