When an electrode (graphite anode, in the examples below) has a certain amount of Lithium ions intercalated, they spread in the material in a regular pattern (more on why does this happen below):

Pictures above (adapted from Liu et al. [1]) illustrate graphite (brown lattice) with Lithium atoms (green balls) intercalated into it. At stage k, Lithium atoms are intercalated at every k-th layer of graphite. The left picture is stage I ($\mathrm{LiC_{6}}$), the right picture is stage II ($\mathrm{LiC_{12}}$).

Notice that at stage I ($\mathrm{LiC_{6}}$), not every "honeycomb cell" of the carbon layer has a Lithium atom on top of it. That would be a superdense $\mathrm{LiC_{2}}$ stage that doesn't occur in battery cells under normal conditions.

In these different regular stage structures, Lithium atoms have different chemical potentials, determined by the quantum system solutions (see density functional theory).

Plateaus of the open-circuit voltage function of an electrode do NOT correspond to the chemical potentials of ion intercalation at different stages

Why do Lithium atoms intercalate only in every k-th interlayer (as long as there are sufficiently few atoms intercalated) leaving other graphite interlayers empty?

Weaker intra-layer attraction leads to a smoother open-circuit voltage function without plateaus

Related:

• LTO lattice structure

References

[1] Kinetically Determined Phase Transition from Stage II ($\mathrm{LiC_{12}}$) to Stage I ($\mathrm{LiC_{6}}$) in a Graphite Anode for Li-ion Batteries (2018)

[2] A Lattice-Gas Model Study of Lithium Intercalation in Graphite (1999)