The Southern Ocean has been identified as a key player for the global atmospheric temperature and pCO2 rise across the last glacial termination. One leading hypothesis for explaining the initial pCO2 step of 38 ppm (Mystery Interval 17.5 – 14.5 ka) is enhanced upwelling of Southern Ocean deep water that had stayed isolated from surface layers for millennia, thereby accumulating carbon from remineralisation of organic matter. However, the individual influences involved in this interplay of processes are not fully understood. A credible explanation for this remarkable climate change must also be able to reproduce a simultaneous steep decrease of carbon isotope ratios (δ13C and ∆14C). To address this topic, we here apply the Danish Center for Earth System Science (DCESS) Earth System Model with an improved terrestrial biosphere module and tune it to a glacial steady-state within the constraints provided by various proxy data records. In addition to adjustments of physical and biogeochemical parameters to colder climate conditions, a sharp reduction of the oceanic mixing intensity below around 1800 m depth in the high latitude model ocean is imposed, generating a model analogy to isolated deep water while maintaining this water oxygenated in agreement with proxy data records. From this glacial state, transient sensitivity experiments across the last glacial termination are conducted in order to assess the influence of various mechanisms on the climate change of the Mystery Interval. We show that the upwelling of isolated deep water in the Southern Ocean complemented by several physical and biogeochemical processes can explain parts but not all of the atmospheric variations observed across the Mystery Interval.