<div><b>Endowed with a multitude of exquisite properties such as rich electrochemistry, superb topology and eccentric electromagnetic phenomena, honeycomb layered oxides have risen to the top echelons of science with applications in diverse fields ranging from condensed matter physics, solid-state chemistry, materials science, solid-state ionics to electrochemistry. Although these features are known to stem from the utilitarian structure innate in these oxides, their functionalities are vastly underutilised as their underlying atomistic mechanisms remain unknown. Therefore in this study, atomic resolution imaging on pristine K<sub>2</sub>Ni<sub>2</sub>TeO<sub>6 </sub>along multiple zone axes were conducted using spherical aberration-corrected scanning transmission electron microscopy (Cs-corrected STEM) to reveal hitherto unreported topological defects and curvature which can be associated with various phase transitions. Furthermore we discover, <i>for the first time</i>, the occurrence of a new stacking variant with P3-type sequence alongside the well-reported P2-type stacking domains. Through this work, we provide insights into the connection between these unique structural disorders to the electrochemical properties of honeycomb layered oxides. The mechanism of the phase transitions reported herein is bound to become apparent upon high alkali-ion mobility, providing invaluable clues to potentially improve their functional performance in, for instance, energy storage applications. Our findings have the potential to inspire further experimental and theoretical studies into the role of stacking and topology in honeycomb layered oxides.</b></div>