Preheat oven to 375 F. Poke holes in spaghetti squash with a knife and microwave for 5 minutes, then slice in half horizontally (the short way) and remove the seeds. Place the spaghetti squash, cut side down on a rimmed baking sheet with 2 tablespoons of water. Roast spaghetti squash on top rack for 20-30 minutes or until strands are just cooked enough to pull from the shell.
While the squash is roasting, place the feta cheese in the middle of an 8X12 baking dish. Arrange the tomatoes, mushrooms and garlic around the cheese. Drizzle with olive oil and season with red pepper flakes, black pepper, and half the fresh basil. Place the baking dish on the bottom rack of the oven and roast for 20-30 minutes, or until the tomatoes are bursting and the feta is golden on top. Add the remaining basil and mix.
When the squash is finished, pull the strands with a fork and place them in the baking dish with the feta cheese and vegetables. Mix until fully combined. Add a squeeze of lemon juice and garnish with more fresh basil if you like.