Heat the olive oil in a large skillet over medium heat.
Add the shallot and crushed red pepper flakes and cook, stirring often, for 2 minutes.
Add the minced garlic and cook, stirring constantly, for 30 seconds.
Add the crushed tomatoes and lower heat to low; simmer for 30 minutes making sure to stir occasionally.
Taste and season with sea salt and freshly cracked pepper, to taste.
Cook the gnocchi in salted boiling water, per package instructions, about 3 minutes; drain, reserving 1/4 cup of cooking water.
Add the drained gnocchi to the tomato sauce and a bit of the cooking water if needed.
Add most of the fresh basil and toss to coat evenly.
Place into a serving bowl and add bits of mozzarella cheese, remaining basil, and freshly grated Parmesan.
Serve and enjoy.