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Adjust rack to top position and preheat oven to 425 degrees. Wash and dry produce.
Halve, peel, and thinly slice ¼ of the onion; dice remaining onion. Zest and quarter lime (for 4 servings, zest one lime and quarter both). Halve green peppers lengthwise; remove stems and seeds. Dice tomato and season with a pinch of salt and pepper.
In a small microwave-safe bowl, combine sliced onion, juice from half the lime, ¼ tsp sugar (½ tsp for 4), and a pinch of salt. Microwave until onion is bright pink, 30 seconds. Set aside to pickle.