  We prove that a sequence of Fueter sections of a bundle of compact
hyperkahler manifolds $\mathfrak X$ over a $3$-manifold $M$ with bounded energy
converges (after passing to a subsequence) outside a $1$-dimensional closed
rectifiable subset $S \subset M$. The non-compactness along $S$ has two
sources: (1) Bubbling-off of holomorphic spheres in the fibres of $\mathfrak X$
transverse to a subset $\Gamma \subset S$, whose tangent directions satisfy
strong rigidity properties. (2) The formation of non-removable singularities in
a set of $\mathcal H^1$-measure zero. Our analysis is based on the ideas and
techniques that Lin developed for harmonic maps. These methods also apply to
Fueter sections on 4-dimensional manifolds; we discuss the corresponding
compactness theorem in an appendix. We hope that the work in this paper will
provide a first step towards extending the hyperkahler Floer theory developed
by Hohloch-Noetzl-Salamon to general target spaces. Moreover, we expect that
this work will find applications in gauge theory in higher dimensions.
