Magnetic, bathymetric, and SeaMARC II side scan sonar data from the ridge flanks adjoining the overlapping spreading center (OSC) at 9°03′N on the East Pacific Rise (EPR) are used to establish the evolution of this ridge axis discontinuity and adjacent ridge segments within the past 2.4 m.y. A three‐dimensional inversion for magnetization shows the discontinuity evolved from one of small offset (2 km) to an 8‐km offset OSC within the past approximately 1.0 m.y. The OSC has left a v‐shaped discordant zone indicating an average southward migration of 42 km/m.y. since the beginning of anomaly 2 time (1.8 m.y.). The west flank discordant zone consists of discrete abandoned overlap basins bounded by highly magnetized ridge tips with anomalous lineations, while the east flank discordant zone is a broad swath of high magnetization, anomalous lineations, and greater depths. Kinematic modelling indicates that southward migration has not been steady but has been accomplished by a series of episodic propagation events with rates ranging from <10 mm/yr to >500 mm/yr. Ridge tips have been abandoned at intervals of approximately 50,000–100,000 years both by linkage of neighboring ridge segments and by self‐decapitation. Magnetic modelling suggests rotations of overlap basins of >25°, consistent with predictions of kinematic modelling. Orientation of magnetic isochrons indicate a 3°–6° counterclockwise change in Pacifie‐Cocos plate motion within the past ∼1 m.y., assuming orthogonal spreading throughout this time. Although the discontinuity currently located at 9°03′N existed prior to this change in plate motion, its growth into a right‐stepping, 8‐km offset OSC may be causally related to this change. The current configuration of intratransform spreading within the Siqueiros has developed since onset of the Brunhes anomaly (0.73 m.y.) possibly in response to this recent counterclockwise change in plate motion. In addition to the OSC, there is evidence for several small discontinuities offsetting the ridge during anomaly 2 time, which have since migrated along the ridge and vanished. An axial magnetization high is observed along the crest of the EPR. Change in the magnitude of the axial magnetization high or shifts in its location relative to the bathymetric axis coincide with several devals within the area. Magnetization maxima are found at ridge transform intersections and the OSC. These highs may reflect presence of highly fractionated FeTi basalts erupted from magma chambers with restricted supply located adjacent to both large‐and short‐offset ridge axis discontinuities. Discrete magnetization highs are found off‐axis adjacent to Clipperton and Siqueiros fracture zones, indicating that production of FeTi basalts at ridge‐transform intersections is episodic. Magnetizations are higher north of Clipperton than south of it, possibly reflecting a long‐lived starvation in magma supply north of Clipperton, and more abundant supply to the south. Most seamounts within the area have the same magnetization polarity as surrounding seafloor, indicating that seamount formation occurs near the ridge axis. The exceptions lie near magnetic reversal boundaries and are consistent with seamount formation as close as 10 km from the ridge axis. Few pronounced magnetization highs are associated with seamounts, indicating that the magnetized source layer is no thicker beneath them than surrounding seafloor or that seamount basalts are substantially less magnetic than normal mid‐ocean ridge basalts.