The stability of the jet in cross-flow is investigated using a complete set-up including the flow inside the pipe. First, direct simulations were performed to find the critical velocity ratio as a function of the Reynolds number, keeping the boundary-layer displacement thickness fixed. At all Reynolds numbers investigated, there exists a steady regime at low velocity ratios. As the velocity ratio is increased, a bifurcation to a limit cycle composed of hairpin vortices is observed. The critical bulk velocity ratio is found at approximately $R=0.37$ for the Reynolds number $Re_{D}=495$, above which a global mode of the system becomes unstable. An impulse response analysis was performed and characteristics of the generated wave packets were analysed, which confirmed results of our global mode analysis. In order to study the sensitivity of this flow, we performed transient growth computations and also computed the optimal periodic forcing and its response. Even well below this stability limit, at $R=0.3$, large transient growth ($10^{9}$ in energy amplification) is possible and the resolvent norm of the linearized Navier–Stokes operator peaks above $2\times 10^{6}$. This is accompanied with an extreme sensitivity of the spectrum to numerical details, making the computation of a few tens of eigenvalues close to the limit of what can be achieved with double precision arithmetic. We demonstrate that including the meshing of the jet pipe in the simulations does not change qualitatively the dynamics of the flow when compared to the simple Dirichlet boundary condition representing the jet velocity profile. This is in agreement with the recent experimental results of Klotz et al. (J. Fluid Mech., vol. 863, 2019, pp. 386–406) and in contrast to previous studies of Cambonie & Aider (Phys. Fluids, vol. 26, 2014, 084101). Our simulations also show that a small amount of noise at subcritical velocity ratios may trigger the shedding of hairpin vortices.