In a large skillet, heat olive oil over medium-high heat. When the oil starts to shimmer, add the chopped onion, garlic and red pepper flakes. Cook, stirring, occasionally, for about 3 minutes, just until the onion starts to soften.
Meanwhile, bring a large pot of water to boil over high heat. When it reaches a rolling boil, add the whole grain spaghetti. Cook spaghetti according to package directions.
Add the halved grape tomatoes to the sauteed onions. Stir to coat the tomatoes in the oil and continue cooking, so tomatoes soften. This should take about 8 minutes, about the length of time it will take for the pasta to become al dente. Stir the lentils in with the tomatoes.
Drain the pasta, reserving 1 cup of the pasta cooking water. Return the pasta to the pot. Add the tomatoes and lentils and pasta water. It has a beautiful starchiness, which, combined with the pasta, tomatoes and lentils, thickens into a spaghetti-hugging sauce. Stir well together.
Add the chopped basil and arugula by the handful, combining just until the greens wilt. Season generously with sea salt and freshly ground pepper. Enjoy at once.