The discovery of graphene has attracted significant attention and research on the material as well as providing avenues of research into other two-dimensional (2D) materials. Expanding the properties of graphene requires integration with other systems, such as molecules, or other low dimensional materials, to provide new functionalities and applications. In particular, the strong sp2 bond between carbon atoms in graphene gives a unique opportunity for adatom adsorption. Decorating the surface of graphene with adatoms and nanoclusters is one approach that can alter the band structure of graphene and introduce dopants that can modify the p-type and n-type behavior. Moreover, the integration of other 2D materials with graphene can significantly alter their properties and also lead to observation of new structure or phenomenon. The first chapter is based on synthesizing, extracting and separating endohedral metallo-fullerenes (EMFs) and their integration with 2D graphene systems. Optimal set of process parameters for the arc discharge apparatus for the production of EMFs was identified along with the best solvent extraction and separation methodologies. The EMFs studied were La@C82, Y@C82, Sc3N@C80 and Gd3N@C80. EPR was used to confirm purity and characteristics of the EMFs. Gd based metallofullerene (Gd3N@C80) molecules was then used to integrate with the graphene system and used to create single adatoms and nanoclusters on a graphene surface. An in-situ heating holder within an aberration corrected scanning transmission electron microscope was used to track the adhesion of endohedral metallofullerenes to the surface of graphene, followed by Gd metal ejection and diffusion across the surface. Hydrogen was shown to be used to reduce the temperature of EMF fragmentation and metal ejection, enabling Gd nanocluster formation on graphene surfaces at temperatures as low as 300oC. The second part of the project was to study the other 2D materials in their heterostructures with graphene. Lead Iodide (PbI2) is a large band gap 2D layered material that has potential for 2D semiconductor applications. However, atomic level imaging of PbI2 monolayer crystal structure and its fundamental defects has been limited due to challenges in obtaining suitable quality thin crystals. In this work, liquid-exfoliation was used to produce monodisperse 2D monolayer PbI2 nanodisks (30-40nm in diameter and >99% monolayer purity) and deposit them onto suspended graphene supports that have high electron beam transparency to enable atomic resolution annular dark field scanning transmission electron microscopy (ADF-STEM) of PbI2. Strong epitaxial alignment of PbI2 monolayers with the underlying graphene lattice occurred, with PbI2 zig-zag edge commensurate with the graphene arm-chair edge direction, leading to a phase shift from the 1T to 1H structure to increase the level of commensuration in the two lattice spacings (PbI2 and graphene). Then the fundamental point vacancy structures in PbI2 monolayers were imaged directly, showing rapid vacancy migration to the edges and self-healing. Zig-zag edges were also observed to dominate the PbI2 nanodisks. Nanopores were produced by electron beam irradiation of the PbI2 nanodisks and they underwent migration as an intact entity throughout the lattice. These results provided a detailed insight into the atomic structure and defects in monolayer PbI2, and the impact of the strong van der Waals interaction with graphene, which has importance for future applications in opto-electronics. The third chapter studies the role of graphene in another newly emerging 2D material, Palladium Diselenide (PdSe2). Technologically challenging, controllable transformation between the semiconducting and metallic phases of transition metal chalcogenides (TMDs) is of particular importance. Here, controlled laser irradiation could be used to ablate PdSe2 thin films using high power, or trigger the local transformation of PdSe2 into a metallic phase PdSe2-x using lower laser power. PdSe2 material demonstrated strong sensitivity to laser exposure where high laser power resulted in local material degradation and formation of Pd nanoparticles (NPs), while lower laser power could be used to controllably modify the PdSe2 phase, making it Se-deficient and resulting in a PdSe2-x phase. Four regions within the film were observed after laser exposure (1) hole region where the PdSe2 film and graphene were fully damaged, (2) PdSe2 film was modified forming Pd NPs; (3) the phase change of the material was observed where PdSe2 transforms into PdSe2-x and (4) unmodified area of PdSe2. The presence and absence of graphene considerably changed the hole formation area and the phase transformation.