Place lentils in a medium saucepan and cover with at least 2” of water. Boil until tender (about 20 minutes), drain and reserve.
While the lentils are cooking, make the Bolognese. Heat a large saucepan over medium heat. Add the olive oil and onions. Cook until softened and translucent (about 5 minutes). Add the garlic, thyme and tomato paste. Stir to lightly caramelize the tomato paste and allow the garlic and thyme to become aromatic (about 1 minute). Add the red wine, bay leaf, pepper flakes and tomatoes. Break up the tomatoes using a whisk or clean kitchen scissors. Bring to a simmer and cook until the flavors have melded and the sauce has thickened (about 20 minutes). Stir in the lentils. Taste and adjust seasoning.
While the Bolognese is simmering, bring a large pot of salted water to a boil. Cook the rigatoni according to package directions. Drain.
Divide rigatoni between 4 bowls and top with sauce. Sprinkle with basil.