In a large pot over medium-low heat, melt butter. Add onions and caramelize, stirring occasionally, until deeply golden, 15 minutes. Season with salt and pepper.
Add garlic, thyme, and French onion soup mix to pot and stir until garlic is fragrant, 1 minute.
Add penne, beef broth, and water and bring to a boil, then let simmer until penne is al dente and most liquid is absorbed (it should be saucy), 18 to 20 minutes.
Add heavy cream and 1 cup gruyère and stir until cheese is melted.
Serve as is, or serve like French onion soup: Heat broiler. Transfer pasta to oven-safe bowls or ramekins and top with remaining gruyère. Broil until cheese is melted, 1 to 2 minutes, then garnish with more thyme and serve immediately.
Recipe by 5* trending recipes with videos at https://food.theffeed.com/2019/01/16/french-onion-penne/