We study how close-in systems such as those detected by Kepler are affected by the dynamics of bodies in the outer system. We consider two scenarios: outer systems of giant planets potentially unstable to planet-planet scattering and wide binaries that may be capable of driving Kozai or other secular variations of outer planets' eccentricities. Dynamical excitation of planets in the outer system reduces the multiplicity of Kepler-detectable planets in the inner system in ~20-25 per cent of our systems. Accounting for the occurrence rates of wide-orbit planets and binary stars, ≈18 per cent of close-in systems could be destabilized by their outer companions in this way. This provides some contribution to the apparent excess of systems with a single transiting planet compared to multiple; however, it only contributes at most 25 per cent of the excess. The effects of the outer dynamics can generate systems similar to Kepler-56 (two coplanar planets significantly misaligned with the host star) and Kepler-108 (two significantly non-coplanar planets in a binary). We also identify three pathways to the formation of eccentric warm Jupiters resulting from the interaction between outer and inner systems: direct inelastic collision between an eccentric outer and an inner planet; secular eccentricity oscillations that may 'freeze out' when scattering resolves in the outer system; and scattering in the inner system followed by 'uplift', where inner planets are removed by interaction with the outer planets. In these scenarios, the formation of eccentric warm Jupiters is a signature of a past history of violent dynamics among massive planets beyond ~1 au.