  We show that relations in Homflypt type skein theory of an oriented
$3$-manifold $M$ are induced from a $2$-groupoid defined from the fundamental
$2$-groupoid of a space of singular links in $M$. The module relations are
defined by homomorphisms related to string topology. They appear from a
representation of the groupoid into free modules on a set of model objects. The
construction on the fundamental $2$-groupoid is defined by the singularity
stratification and relates Vassiliev and skein theory. Several explicit
properties are discussed, and some implications for skein modules are derived.
