The current Mars Sample Return (MSR) mission is poised to return rock samples to Earth from the surface of Mars as early as 2033 – with a major goal of this ground-breaking mission being the investigation of Martian biology. In response to the preparation and development required for a successful MSR mission, this project aims to both further the understanding of Martian habitability and prepare for the analysis of returned samples in a biological context. An extensive literature compilation of 11 nakhlite Martian meteorites is produced including the bulk rock compositions, iddingsite compositions, and crystallisation ages. Evidence is presented supporting both a low water-rock ratio ephemeral interaction and a high water-rock ratio potentially long-lived hydrothermal environment as the true nature of the Nakhlite launch site’s aqueous alteration. An ephemeral alteration is ultimately favoured. Atom probe tomography (APT) analyses of the nakhlite Northwest Africa 817 illuminate that, given more attention, APT holds the potential to assist in distinguishing between these two end-case scenarios for the nakhlite alteration (which present greatly differing habitability potentials). An analytical pipeline is successfully employed to directly probe nm-scale carbon inclusions preserved within fossiliferous Rhynie chert and Yellowstone National Park samples (both known terrestrial analogue sites resembling Martian hydrothermal environments). The methodology and analytical avenues presented in these terrestrial analogue investigations can serve as a guide for future returned Martian sample interrogations in the search for preserved Martian biosignatures. Along with evaluating the analytical workflow’s effectiveness, multiple recommendations are proposed to improve the pipeline in response to issues experienced throughout this project – developing the pipeline such that better, more robust, results may be obtained in future utilisations. This work carries MSR implications, embodying a step towards the preparation for the analysis of returned Martian samples in a biological context, and also serves to advocate for the usage of APT in the analysis of Martian meteorites, returned Martian samples, and further planetary science materials.