Cut both ends of squash off 1/2 - inch then cut squash in half. Scoop out seeds and discard.
Brush inside of each squash halve with 1/4 tablespoon olive oil and sprinkle with 1/2 teaspoon salt and pepper each. Place squash on baking sheet and bake for 40 minutes to an hour or until inside meat is tender.
In medium pan, heat 3 tablespoons oil. Add onions and saute for 3 minutes or until translucent.
Add chicken, apples, thyme, 1 teaspoon of salt and pepper each, and saute for 5 minutes or until apples are slightly tender. Remove from heat and set aside.
Once squash has finished baking, remove squash from oven and spoon each half with chicken mixture until the squash is filled.
Return to oven and bake an additional 15 minutes. Remove from oven and serve immediately.