In a large pot of salted boiling water, add the whole wheat spaghetti and cook according to package instructions until al dente. Reserve about 1/2 cup of pasta water, then drain the rest and set the pasta aside.
In the same pot, heat the olive oil over medium heat. Add minced garlic and sauté for about 1 minute until fragrant. Be careful not to burn the garlic.
Stir in the halved cherry tomatoes and cook for about 5-7 minutes until they start to blister and soften.
Add in the chopped spinach, red pepper flakes, salt, and black pepper. Cook for an additional 2-3 minutes, stirring until the spinach wilts and combines.
Return the drained spaghetti to the pot and add the reserved pasta water gradually while tossing to combine everything. This will help create a light sauce.
Stir in the fresh basil, lemon zest, and adjust seasoning if necessary. If desired, sprinkle with grated Parmesan cheese before serving.
Serve the pasta in bowls, garnishing with additional basil leaves and a drizzle of olive oil for a vibrant presentation.