Preheat the oven to 375°F.
Poke holes in the spaghetti squash with a fork. Place on a baking sheet and bake for 60–75 minutes, or until soft to the touch. Remove from the oven, cut in half, and allow to cool.
Meanwhile, heat the olive oil in a large sauté pan over medium heat. Add the shallot and mushrooms. Cook, stirring occasionally, until the mushrooms are soft and have released their liquid.
Add the red pepper and cook for 3–4 minutes more, until the pepper is soft. Add the spinach and cook, stirring occasionally, until the spinach is wilted.
Stir in ½ teaspoon oregano, ½ teaspoon red pepper flakes, and ¼ teaspoon salt.
Remove the seeds from the squash. Run a fork lengthwise along the squash to remove the spaghetti-like strands.
Place the squash in a clean tea towel. Wring any excess water from the strands (keep wringing until no more water escapes) and place into a bowl. Season with ½ teaspoon salt and toss until combined.
Combine the ricotta, ½ cup of the Italian blend cheese, milk, basil, and remaining ¼ teaspoon salt in a medium bowl. Stir until combined.
Raise the temperature of the oven to 400°F.
To assemble, grease an 8x8 inch baking dish. Pour ½ cup of marinara sauce into the bottom. Top with ⅓ of the squash. Spread ½ of the ricotta mixture on top, followed by ½ of the vegetables.
Repeat steps by topping with another ⅓ of the squash, the remaining ricotta, and the remaining vegetables.
Top with the final ⅓ of the squash, then pour the remaining marinara sauce over the top. Sprinkle the remaining Italian blend cheese. Place several toothpicks in the top of the lasagna and cover with foil. This will prevent the cheese from sticking to the foil. Bake for 30 minutes.
Remove the foil and turn on the broiler. Broil for 6–8 minutes, or until the cheese is golden brown in spots.
Remove from the oven and let cool for 10 minutes. Garnish with additional fresh basil, slice, and serve.