Preheat oven at 400 degrees Fahrenheit. Grease a deep rectangular baking dish (9x13) and set aside.
Boil water and cook the penne pasta not more than 10 minutes. Make sure not to fully cook the pasta. Leave a little bit of crunch to it so it won't get overcook when you bake it later.
While your pasta is cooking, heat oil in a pan over medium heat. Brown the ground beef. Add onions and garlic. Cook until translucent and fragrant. Get rid of the excess oil - important!
Add the marinara sauce. Add salt and pepper to taste. You may add brown sugar to balance the taste (optional).
Drain pasta and transfer to the baking dish. Pour in the sauce mixture. Toss. Add 1/2 cup of the shredded cheese. Toss again.
Top pasta with the remaining cheese making sure the top is fully covered with cheese. Bake for 10 minutes. You can broil for a minute or 2 before serving.