Position an oven rack in the middle and heat the oven to 425°F. Toss the fennel and onions with olive oil, salt, and pepper on a rimmed baking sheet. Roast until the vegetables are tender and lightly browned, 15 to 20 minutes, stirring halfway through for even coloring.

Bring a large pot of water to a boil. Add the pasta and salt, cooking until al dente—the pasta should still have a slight bite. Drain well and transfer the pasta to a large bowl.

Whisk the lemon zest, lemon juice, garlic, and salt together in a small bowl. Slowly drizzle in the remaining olive oil while whisking constantly to create a smooth, emulsified dressing.

Stir the lemon dressing, roasted vegetables, and tomatoes into the hot pasta. Let the mixture sit at room temperature for about 30 minutes; this allows the pasta to drink up the vinaigrette as it cools.

Fold in the fresh basil just before serving. Taste and adjust with additional salt and pepper as needed.