We show that integrating out M2 branes ending on M5 branes inside Calabi-Yau manifolds captures non-perturbative open topological string physics. The integrating out is performed using a contour integral in complexified Schwinger proper time. For the resolved conifold, this contour can be extended to include the zero pole, which we argue captures the ultraviolet completion of the integrating out and yields the tree-level polynomial terms in the free energy. This is a manifestation of the Emergence Proposal, and provides further evidence for it. Unlike the case of closed strings, where the emergent terms are kinetic terms in the action, for these open strings it is tree-level potential terms which are emergent. This provides a first quantitative example of the proposal that classical tree-level potentials in string theory emerge from integrating out co-dimension one states.