The paper concerns the geochemical analysis of rocks from the ore-bearing layered intrusions that belong to two age groups of the Monchepluton and the Imandra–Umbarechka Complex (2.50 and 2.44 Ga) and the largest gabbro-anorthosite of the Main Ridge Complex (2.51–2.45 Ga). The intrusion of these complexes happened at different depths when the endogenous and geodynamic settings changed at the beginning of the Paleoproterozoic Era. Five megacycles are distinguished in a generalized cross-section of the two-chamber Monchepluton. The megacycles differ in rock composition, rock geochemical features, and mineralization types, i.e., the chromite, sulfide Cu–Ni–PGE and low-sulfide PGE types. The abrupt changes in isotope indicators (εNd, 87Sr/86Sr) mark their boundaries. At a depth of 2037–2383 m, the M-1 borehole intersects a standalone intrusive body that is essentially a magma feeder channel. The intrusive body’s geochemical characteristics and U–Pb isotope age correlate to the Monchepluton rocks. The gabbro-anorthosite massifs united in the Main Ridge Complex were intruded in the following order: the Monchetundra, Chunatundra, Volchetundra, and Losevo–Medvezhye tundras. The largest Monchetundra massif was formed as a result of multiple intrusions of mafic magmatic melt from the deep reservoirs. The melts intruded in two stages, i.e., 2.51–2.49 Ga and 2.48–2.47 Ga, and their composition changed gradually. The gabbro-pegmatites and coeval harrisite dykes are more recent ones (2.46–2.45 Ga). The summarized results of the U–Pb, Sm–Nd, and Re–Os systems research allowed us to establish genetic relations between the studied geological objects. We proposed a model where there was an uplift of a mantle plume to the lower crust area at the age of 2.5 Ga, the deep mantle reservoirs were formed, and a large-scale interaction happened between the parental magma and granulite–eclogite complex rocks. Local contamination and assimilation processes took place during the uplifting of magmas in areas where the magmatic feeding system contacted the host amphibolite–gneiss Archean complexes.