Understanding how Lithium is driven into layer materials such as graphite and the transition metal dichalcogenides (TMDs) is critical in optimizing performance in lithium-ion batteries (LIBs). Understanding how these processes change if Li is replaced by Na will be important if Na is ever to replace Li. The large interlayer spacing in, e.g., MoS2 (∼0.65nm), can accommodate species such as alkali metal ions (Li+/Na+/K+) during the intercalation reaction. Intercalation is reported to change the electronic structure of the host molecule, resulting in variations in their electrical and optical properties. However the solid-state reactions between Li and MoS2 have not been examined in atomistic detail. It is universally accepted that Li+ ions can be inserted into vdW gap but just how this reaction proceeds is still unclear. Plan-view imaging has been extensively used, but really it is essential to visualize the process with the electron beam being parallel to the basal planes of the layer material. Lattice-fringe images have actually been considered for several systems by microtoming specimens or simply using curved regions of the specimen; until the present work the orientation of the specimen was less than ideally uncontrolled. In the present study, TEM specimens are made using FIB, and oriented to allow direct observation of the basal planes. This study of reactions uses both a Tecnai F30 and a Cs/image-corrected Titan equipped with a direct electron detector camera, K2. This camera has two major advantages: the electron dose can be minimized and quick changes during reactions are recorded; a second ChemiSTEM Titan is equipped with both EELS and XEDS capabilities. As the reaction between MoS2 and Li proceeds, white-line defects have been observed using HRTEM. Lower-magnification images show that the defects are not equally spaced and do not correspond to ‘stage’ development. In fact, these defects can cross several basal planes in the MoS2 (either forwards or backwards), this breaking covalent bonds within the layers but maintain essentially the same width after the step; they are not completely constrained to the vdW gap. Density functional theory (DFT) simulations are carried out to investigate the structural accommodation of the layered material during insertion and exertion of the intercalating species (energy barriers, volumetric expansion, and phase transformations). The structural stability of the 2H and 1T phases of MoS2 during lithiation suggests that a phase transformation of the 2H phase of MoS2 to the 1T phase may occur when MoS2 is reacted with Li; the computational study allows different dosages of Lithium ion to be assessed with the aim of testing these the validity of these models using in-situ characterization of the solid-state reactions between Li and MoS2 in the transmission electron microscope (TEM). The role of atomic scale bonding on the energetics and mechanisms of strain relaxation (and phase transformation) due to Li/Na/K intercalation in MoS2, MoSe2, WS2 and WSe2 at the atomic scales will be presented. This work is funded by NSF GOALI grant No. 1820565. MTJ is now at Los Alamos National Laboratory (LANL), WBM is now at Sandia National Laboratories (SNL). The TEM was all carried out at CINT, an Office of Science User Facility operated for the U.S. DOE, or in SNL. SNL is a multi-mission laboratory managed and operated by National Technology and Engineering Solutions of Sandia, LLC., a wholly owned subsidiary of Honeywell International, Inc., for the U.S. DOE’s NNSA under contract DE-NA-0003525. The views expressed in the abstract do not necessarily represent the views of the U.S. DOE or the U.S. Government.