story
While admitting the rest of this thread is bonkers, I'll explicitly list the formula you should follow right now (science is always evolving): Change in Body Stores = (Actual Calories In - Calories Not Absorbed) - (Resting Metabolic Rate + Thermic Effect of Eating + Physical Activity + Non-Exercise Activity Thermogenesis)
This is the more nuanced formula of calories in, calories out. Changing one variable in that equation can have an effect on the rest of the equation, which is why it appears calories is not equal to calories out. You can read about each variable here: http://www.precisionnutrition.com/metabolic-damage.
I should note that this program is published in scientific journals: http://www.invent-journal.com/article/S2214-7829(16)30006-9/... http://link.springer.com/article/10.1007/s11764-016-0582-z http://onlinelibrary.wiley.com/doi/10.1002/osp4.98/abstract