Analog models were used to investigate the influence of cross-trending basement faults on inverted rift systems similar to those located in the Makassar Straits. Multilayer models composed of sand, silicone putties, and a silicone-plasticine mixture were constructed so that laterally offset rift basins would form on either side of a preexisting basement fault. Transfer zones comprising a series of en echelon normal faults that connect downward with the basement fault formed to link the laterally offset rift basins during the extension phase. Subsequent oblique inversion of the models resulted in a general progression starting with broad folding, followed by the development of small-scale inversion anticlines associated with reactivated rift faults, to thrust faulting, and finally, to the formation of cross-trending wrench faults. Rift fault reactivation and wrench fault development were prominent in the transfer zones because of the orientation of the constituent faults (oblique to the shortening direction) and their connection with the underlying basement fault. The addition of an intrasedimentary detachment layer, which represents a thick overpressured shale present in the vicinity of the economically important Mahakam delta, allowed gravitational collapse and extensional faulting to occur on structural highs. The cross-trending basement fault was again the locus for inversion structures, both above and below the detachment layer in the latter case, which may have influenced the distribution of petroleum in the region.