The contributions in magnetic confinement fusion theory presented at the 29th Fusion Energy Conference (FEC 2023) are summarized here. This summary aims at providing an overview of the advances in the field and new directions in integrated modeling, computational physics, control design and application of artificial intelligence to discharge design and optimization. Given the increasing interest in bringing fusion to the grid and the focus on design and discharge optimization by means of self-consistent simulations that integrate physics and engineering with a hierarchy of fidelity models, the layout of this summary highlights applications over fundamental theory.