When Energy Is Used Is It Gone Forever?

If it is an isolated system, then according to the second law of thermodynamics, it should decrease its entropy and continues to reach a thermal equilibrium. Energy is never lost nor created, so no, heat is not the final stage of energy that is wrong. The universe too will one day reach to its maximum entropy and there will no longer be any free energy for matter to interact with to perform work. But the energy of the universe will always remain the same. It is the disorderly of different energy states that allows free energy to be harnessed, for example, two adjacent rooms with a door in the middle having different temperature, the other being hotter while the other is colder, the moment the door is opened, hot air from the room will move to the colder room as what we observe as wind, that motion of air particles from hot to cold is free energy which can be used to perform work. Overtime, the temperature of the two rooms will equalize and there will no longer be any free energy to use. Say, at the beginning they have a room temperature of 30 C and 20 C, they have a difference of 10 C, therefore they are not a their thermal equilibrium, overtime they will settle to a final temperature (25 C) to follow the second law. The universe at its infancy was in a thermodynamic equilibrium, but because of quantum fluctuations, some areas had more matter than the other, causing an imbalance in the gravitational forces allowing the entropy of the universe to decrease, overtime the entropy of the universe will (or might have) reach minimum and will eventually increase as the system balances itself to a thermal equilibrium.