Robots need to have a memory of previously observed, but currently occluded objects to work reliably in realistic environments. We investigate the problem of encoding object-oriented memory into a multi-object manipulation reasoning and planning framework. We propose DOOM and LOOM, which leverage transformer relational dynamics to encode the history of trajectories given partial-view point clouds and an object discovery and tracking engine. Our approaches can perform multiple challenging tasks including reasoning with occluded objects, novel objects appearance, and object reappearance. Throughout our extensive simulation and real-world experiments, we find that our approaches perform well in terms of different numbers of objects and different numbers of distractor actions. Furthermore, we show our approaches outperform an implicit memory baseline.