Preheat your oven to 400°F (200°C) and line a large rimmed baking sheet with parchment paper.
Dice the red bell pepper, zucchini, and red onion into uniform half-inch pieces.
Place the vegetables on the baking sheet, drizzle with olive oil, and sprinkle with half of the sea salt and black pepper.
Roast the vegetables for 15 to 20 minutes until they are tender and show slight caramelization on the edges.
While the vegetables roast, whisk the whole eggs, egg whites, and nutritional yeast in a medium bowl until well combined and slightly frothy.
Heat a large non-stick skillet over medium-low heat and add the ghee, swirling to coat the bottom of the pan.
Pour the egg mixture into the skillet and let it sit undisturbed for about 30 seconds to begin setting.
Using a silicone spatula, gently push the eggs from the edges toward the center, creating soft curds.
When the eggs are about 80% cooked and still look slightly moist, fold in the hot roasted vegetables.
Continue to cook for another 30 to 60 seconds until the eggs are just set, then remove from heat immediately.
Season with the remaining sea salt and black pepper, garnish with freshly chopped chives, and serve immediately.