Preheat oven to 205 degrees Celsius (400 degrees Fahrenheit).
Cut spaghetti squash in half lengthwise. Remove seeds and strands.
Place squash halves in a large baking dish, flesh side up. Drizzle with half the olive oil and season with pepper.
Bake for 40 to 45 minutes, until the flesh is tender and flakes easily with a fork.
Meanwhile, heat the remaining olive oil in a frying pan over medium heat. Cook the onion, bell pepper, and half the pepperoni for 1-2 minutes. Pour in the Normandin spaghetti sauce and bring to a boil. Remove from heat.
Remove squash halves from the oven and shred the flesh with two forks. Top the squash halves with the spaghetti sauce mixture. Add cheese and remaining pepperoni, then sprinkle with thyme.
Bake for 10 to 12 minutes.
Turn the oven to broil and continue baking for 1-2 minutes, until cheese is golden brown.