The 2D layered Ti3C2T2 MXene is known for its diverse chemistry and has been investigated as potential anode and cathode in Li, Na, and Mg batteries. Ti3C2T2 layers can stack in at least two different ways depending on the termination group chemistry. In addition, stacking and termination groups influence the diffusivity and energy of ions intercalated in the MXene. How stacking influences the diffusivity, and how intercalated ions influence the stacking stability are not fully understood. In this study, density functional theory simulations explore Li, Na, and Mg ions intercalated in Ti3C2T2 stacked in four different ways; two are experimentally verified, and previously discussed in literature, and two with limited experimental evidence. It is shown that the stacking can reduce diffusion by 8–20 orders of magnitude. It is also explained how the termination group chemistry and the intercalated Li/Na/Mg ions change the relative stability of the stackings. The stacking's influence on diffusion properties is explained by examining the coordination of the ions at different points along the migration path. It is suggested that Ti3C2T2 with significant fluorine termination can be well‐suited for especially Na anode use, and regardless of termination is unsuited as Mg cathode.