Remove and discard giblets and neck from turkey. Rinse turkey with cold water; pat dry. Trim excess fat. Place turkey in a heavy-duty, jumbo zip-top plastic bag and add 2 cups cider; seal and marinate in refrigerator overnight, turning bag occasionally.
Preheat oven to 450°.
Remove turkey from bag, reserving marinade. Place turkey, breast side up, in a shallow roasting pan. Pour reserved marinade over turkey. Sprinkle 1 teaspoon pepper and 1/2 teaspoon salt on skin and in body cavity. Lift wing tips up and over back; tuck under turkey. Place thyme sprigs and apple in body cavity. Insert meat thermometer into meaty part of thigh, making sure not to touch bone. Cover loosely with foil. Bake at 450° for 10 minutes. Reduce oven temperature to 325° (do not remove turkey from oven); bake an additional 45 minutes. Add 1 3/4 cups broth and onions to pan; return to oven immediately. Bake, uncovered, an additional hour or until thermometer registers 180°. Place turkey on a serving platter; cover with aluminum foil. Let stand at least 25 minutes. Discard skin, sprigs, and apple.
Remove onions from pan with a slotted spoon, set aside, and keep warm. Place a zip-top plastic bag inside a 2-cup glass measuring cup. Pour turkey drippings into bag. Add remaining 1/2 cup cider to roasting pan; cook over medium-high heat 2 minutes, scraping pan to loosen browned bits. Add to turkey drippings in bag; let stand 10 minutes (fat will rise to the top). Seal bag; carefully snip off bottom corner of bag. Drain drippings into a bowl, stopping before fat layer reaches opening; discard fat.
Cook bacon in a large saucepan over medium heat until crisp. Add flour to bacon drippings in pan; cook 1 minute. Gradually add remaining 1 cup broth and cider mixture, blending with a whisk. Stir in 1/4 teaspoon pepper and 1/2 teaspoon salt; cook over medium heat until thick (about 10 minutes), stirring frequently. Stir in onions and chopped thyme.