  In this paper we investigate the large-$N$ behavior of 5-dimensional
$\mathcal{N}=1$ super Yang-Mills with a level $k$ Chern-Simons term and an
adjoint hypermultiplet. As in three-dimensional Chern-Simons theories, one must
choose an integration contour to completely define the theory. Using
localization, we reduce the path integral to a matrix model with a cubic action
and compute its free energy in various scenarios. In the limit of infinite
Yang-Mills coupling and for particular choices of the contours, we find that
the free-energy scales as $N^{5/2}$ for $U(N)$ gauge groups with large values
of the Chern-Simons 't\,Hooft coupling, $\tilde\lambda\equiv N/k$. If we also
set the hypermultiplet mass to zero, then this limit is a superconformal fixed
point and the $N^{5/2}$ behavior parallels other fixed points which have known
supergravity duals. We also demonstrate that $SU(N)$ gauge groups cannot have
this $N^{5/2}$ scaling for their free-energy. At finite Yang-Mills coupling we
establish the existence of a third order phase transition where the theory
crosses over from the Yang-Mills phase to the Chern-Simons phase. The phase
transition exists for any value of $\tilde\lambda$, although the details differ
between small and large values of $\tilde\lambda$. For pure Chern-Simons
theories we present evidence for a chain of phase transitions as
$\tilde\lambda$ is increased.
  We also find the expectation values for supersymmetric circular Wilson loops
in these various scenarios and show that the Chern-Simons term leads to
different physical properties for fundamental and anti-fundamental Wilson
loops. Different choices of the integration contours also lead to different
properties for the loops.
