We give a formalism for constructing hidden sector bundles as extensions of sums of line bundles in heterotic $M$-theory. Although this construction is generic, we present it within the context of the specific Schoen threefold that leads to the physically realistic $B-L$ MSSM model. We discuss the embedding of the line bundles, the existence of the extension bundle, and a number of necessary conditions for the resulting bundle to be slope-stable and thus $N=1$ supersymmetric. An explicit example is presented, where two line bundles are embedded into the $SU(3)$ factor of the $E_{6} times SU(3)$ maximal subgroup of the hidden sector $E_{8}$ gauge group, and then enhanced to a non-Abelian $SU(3)$ bundle by extension. For this example, there are in fact six inequivalent extension branches, significantly generalizing that space of solutions compared with hidden sectors constructed from a single line bundle.
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