Why are some carbon atoms from Carbon Dioxide not incorporated into sugar molecules in darkness?

What is necessary for them to go to a higher phase?

Plants only convert CO2 into other compounds in light where they have the energy to do it. Some plants don't convert it into sugar right away to save water. CO2 has no potential energy. Sugar has approximately 4 kcal of energy per gram. Not sure what higher phase means. It requires energy, complex enzymes, and water to convert CO2 into sugar.

Much of the food ingested into each organism is metabolized in cell respiration. Why is this so? What does the organism need and get out of this process and how does it get it?

It is the most efficient method where the most calories are gained. It gets energy by making ATP which is converted into ADP and gives energy to most every process in the cell that needs energy.