Preheat oven to 375 F. Line a baking sheet with aluminum foil and set aside.
In a small saucepan, heat 1 teaspoon of olive oil over medium heat. Add the shallots to the hot oil and saute until soft and translucent, about 5 minutes. Add apple cider, cider vinegar, and syrup; bring to a boil. Add thyme, reduce heat and simmer 20 minutes.
While the sauce is simmering, rub the cod with the remaining 2 teaspoons of olive oil and season with salt and pepper to taste. Wrap in foil and place on foil-lined baking sheet. Bake for 15 minutes or until fish is done.
Serve cod with cider shallot sauce drizzled on top.