Preheat the oven to 400°F (200°C). Slice the spaghetti squash lengthwise and scoop out the seeds with a spoon.
Brush the cut surfaces of each squash half with about 1 teaspoon of the olive oil and season evenly with 1/4 teaspoon salt and 1/8 teaspoon pepper.
Place the squash halves flesh-side down on a baking sheet and roast until the edges are lightly browned and the flesh is tender, about 45 minutes.
About 10 minutes before the squash is done, heat the remaining olive oil in a large nonstick skillet over high heat.
Add the sliced bell pepper and sliced red onion and stir-fry for 3–4 minutes until slightly charred and softened.
Add the shrimp and 1/2 tablespoon fajita seasoning to the skillet and cook, stirring, until the shrimp are just opaque and cooked through, about 3–4 minutes; remove from heat.
When the squash is roasted, remove from the oven and use a fork to scrape the flesh into spaghetti-like strands directly in the squash halves or into a bowl.
Toss the squash strands with the cooked shrimp and vegetables in the skillet (or combine in a bowl) until well mixed.
Divide the shrimp and squash mixture evenly between the two squash halves, sprinkle 1/2 cup shredded cheese over the top, and return to the oven for about 5 minutes until the cheese melts.
Remove from the oven and serve warm.
