In a large pot, heat olive oil over medium heat. Add garlic and sauté for 1 minute.
Add Swiss chard and sauté for 2 minutes, until starts to wilt. Mix in nutmeg, pepper & salt. Stir and sauté 8 – 10 more minutes, or until chard is completely wilted. Remove from heat and add to a colander. When slightly cooled, squeeze as much liquid as possible out of the chard. Place in a large bowl.
Preheat oven to 400 degrees F.
Stir 2 eggs, ricotta cheese, 3 tablespoons Parmesan cheese and thyme into the Swiss chard, mix until completely incorporated. Mix in flour. Set aside.
Roll out pie dough to fit into 9–inch pie pan. Place in pan and flute the edges. Spread half of the Swiss chard mixture over the pie dough.
Hollow out 6 small oval areas in the Swiss chard mixture to place the cracked eggs. Carefully crack each of the 6 remaining eggs to fit into each hollow.
Carefully spread the remaining Swiss chard mixture over top the eggs. Sprinkle remaining 3 tablespoons of Parmesan cheese on top.
Bake for 25 minutes, then check to see if the pie crust edges are getting brown. Cover the edges of the pie with tin foil to prevent from burning and cook for another 20 minutes or until the filling is completely set (about 45 minutes total.) Remove from oven and let cool 10 minutes before serving.