  T-branes are a non-abelian generalization of intersecting branes in which the
matrix of normal deformations is nilpotent along some subspace. In this paper
we study the geometric remnant of this open string data for six-dimensional
F-theory vacua. We show that in the dual M-theory / IIA compactification on a
smooth Calabi-Yau threefold X, the geometric remnant of T-brane data translates
to periods of the three-form potential valued in the intermediate Jacobian of
X. Starting from a smoothing of a singular Calabi-Yau, we show how to track
this data in singular limits using the theory of limiting mixed Hodge
structures, which in turn directly points to an emergent Hitchin-like system
coupled to defects. We argue that the physical data of an F-theory
compactification on a singular threefold involves specifying both a geometry as
well as the remnant of three-form potential moduli and flux which is localized
on the discriminant. We give examples of T-branes in compact F-theory models
with heterotic duals, and comment on the extension of our results to
four-dimensional vacua.
