
Generic depiction of an "initial state" of a reaction system, at a specific value of energy, which may proceed through any of various reaction pathways, in its course of action towards a "final state", signified by a specific value of energy, at a later point in time (or concentration) on the reaction coordinate. [1]

Generic depiction of an "initial state" of a reaction system, at a specific value of energy, which may proceed through any of various reaction pathways, in its course of action towards a "final state", signified by a specific value of energy, at a later point in time (or concentration) on the reaction coordinate. [1]

In thermodynamics, final state, as compared to an initial state, refers, generally, to the measurement of the free energy or the reactants, graphically shown on the reaction coordinate, at the end or final second at the last stage of the reaction sequence. The two different states, are often explained in terms of differences in the bonding geometries, bonding changes, and bond energies of the products as compared to the reactants.

Overview
In 1993, American chemist Martin Goldstein gave the following example of what is meant by initial versus final in the context of "states", specifically in regards to how one would go about calculating the Gibbs free energy of formation of a mouse (or by extrapolation a human): [2]

“To apply thermodynamics to the problem of how life got started, we must ask what net energy and entropy changes would have been is simple chemical substances, present when the earth was young, were converted into living matter [as in the formation of a mouse] … to answer this question [for each process], we must determine the energies and entropies of everything in the initial state and final state.”

In other words, the initial state is one point in time in the course of the reaction, typically the beginning, or point at which reactant collision occurs, millisecond in which the reaction becomes activated, or time at which the reactants are introduced into the reacting system. The final state is some amount of time (seconds, minutes, days, or years, etc.) following the start of the reaction.

References
1. Wallace, Thomas P. (2009). Wealth, Energy, and Human Values: the Dynamics of Decaying Civilizations from Ancient Greece to America (Appendix A: The Fundamentals of Thermodynamics Applied to Socioeconomics, pgs. 469-89; Graph, pg. 474.). AuthorHouse.
2. Goldstein, Martin and Goldstein, Inge F. (1993). The Refrigerator and the Universe: Understanding the Laws of Energy (section: Entropy of a mouse, pgs. 297-99). Harvard University Press.