Bring a medium pot of salted water to a boil and cook the red lentil penne until al dente, then drain and set aside.
In a large skillet over medium-high heat, add the ground Wagyu beef and sear until deeply browned and cooked through, breaking it into small crumbles.
Remove the beef from the skillet and set aside, leaving approximately one tablespoon of the rendered fat in the pan.
Add the diced yellow onion and sliced cremini mushrooms to the skillet, sautéing until the mushrooms have released their moisture and turned golden brown.
Stir in the minced garlic and fresh thyme, cooking for 60 seconds until the aromatics are fragrant.
Return the cooked Wagyu beef to the skillet and pour in the tomato puree and beef bone broth.
Reduce the heat to medium-low and simmer the mixture for 8 to 10 minutes, allowing the sauce to thicken and the flavors to meld.
Season the ragout with sea salt and black pepper to taste.
Toss the cooked lentil penne into the skillet, stirring gently to coat the pasta in the rich sauce before serving.