The Skaergaard intrusion is a layered, ferrobasaltic intrusion emplaced during the Early Eocene into the rifting volcanic margin of East Greenland. The magma chamber crystallised in response to cooling from the roof and margins upwards and inward, forming upper, marginal and bottom series, the latter referred to as the Layered Series. The phase layering in the bottom series suggests an evolved, olivine-normative tholeiitic melt saturated in plagioclase and olivine, followed by augite, and then simultaneously by ilmenite and magnetite forming primocrysts. Pigeonite appears in the lower parts and continues until the centre of the series. Apatite appears in the upper part concurrently with liquid immiscibility. Cryptic variations of the individual primocrysts record a systematic upward increase in iron and decrease in magnesium for the mafic minerals and a systematic increase in sodium and decrease in calcium for plagioclase. The appearance of pigeonite is caused by reactions and crystallisation in the trapped melt and by subsolidus adjustments without this phase reaching liquidus saturation. The high mode of olivine at the base of the upper part with the appearance of apatite is interpreted to mark the onset of liquid immiscibility. This may have led to the separation of conjugate melts with granophyre migrating upward and the basic component largely staying stationary or sinking. Petrologic and geochemical observations indicate differentiation in the lower part of the intrusion, principally controlled by crystal fractionation with the efficiency of fractionation controlled by the evolution and escape of liquid from the solidifying mush. During the final stages of solidification, the onset of liquid immiscibility and termination of melt convection impeded differentiation. Modelling by perfect Rayleigh fractionation shows that major and included trace elements conform reasonably to observations, while excluded elements deviate from model predictions. This decoupling is caused by the mobility of a granophyre component formed in the trapped melt and in the main residual magma chamber. Consequently, the sampled gabbros may not be representative of the final solid-melt mush. By restoring the gabbros to their original mush compositions, it is possible to constrain granophyre migration pathways. We suggest that the granophyre formed in the trapped melt in the lower part of the intrusion mostly migrated laterally through pressure release pathways to form lenses and pockets with only limited upward migration into the main magma reservoir. Near the end stage of differentiation, the residual magma exsolved and formed complex mixtures of ferrobasaltic and granophyric melts. Estimates predict that a substantial amount of the granophyric melt penetrated as sills into the downward crystallising, upper part of the body as well as into the host rocks. The redistribution of granophyric melts within the solidifying crystal mush complicates predictions of trapped-melt content and mass-balance calculations but helps to explain apparent decoupling of included and excluded trace elements, especially towards the end stages of evolution. Final crystallisation was controlled mostly by in situ crystallisation leaving complex mixtures of ferrodiorite and granophyre components.