Chemical transformation of existing two-dimensional (2D) materials can be crucial in further expanding the 2D crystal palette required to realize various functional heterostructures. In this work, we demonstrate a 2D 'on-stack' chemical conversion of single-layer crystalline MoS2 into MoO3 with a precise layer control that enables truly 2D MoO3 and MoO3/MoS2 heterostructures. To minimize perturbation of the 2D morphology, a nonthermal oxidation using O2 plasma was employed. The early stage of the reaction was characterized by a defect-induced Raman peak, drastic quenching of photoluminescence (PL) signals and sub-nm protrusions in atomic force microscopy images. As the reaction proceeded from the uppermost layer to the buried layers, PL and optical second harmonic generation signals showed characteristic modulations revealing a layer-by-layer conversion. The plasma-generated 2D oxides, confirmed as MoO3 by x-ray photoelectron spectroscopy, were found to be amorphous but extremely flat with a surface roughness of 0.18 nm, comparable to that of 1L MoS2. The rate of oxidation quantified by Raman spectroscopy decreased very rapidly for buried sulfide layers due to protection by the surface 2D oxides, exhibiting a pseudo-self-limiting behavior. As exemplified in this work, various on-stack chemical transformations can be applied to other 2D materials in forming otherwise unobtainable materials and complex heterostructures, thus expanding the palette of 2D material building blocks.