Intercalation of alkali atoms within the lamellar transition metal dichalcogenides is a possible route toward a new generation of batteries. It is also a way to induce structural phase transitions authorizing the realization of optical and electrical switches in this class of materials. The process of intercalation has been mostly studied in three-dimensional dichalcogenide films. Here, we address the case of a single-layer of molybdenum disulfide (MoS$_2$), deposited on a gold substrate, and intercalated with cesium (Cs) in ultra-clean conditions (ultrahigh vacuum). We show that intercalation decouples MoS$_2$ from its substrate. We reveal electron transfer from Cs to MoS$_2$, relative changes in the energy of the valence band maxima, and electronic disorder induced by structural disorder in the intercalated Cs layer. Besides, we find an abnormal lattice expansion of MoS$_2$, which we relate to immediate vicinity of Cs. Intercalation is thermally activated, and so is the reverse process of de-intercalation. Our work opens the route to a microscopic understanding of a process of relevance in several possible future technologies, and shows a way to manipulate the properties of two-dimensional dichalcogenides by under-cover functionalization.
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