Abstract We detect widespread [C ii] 157.7 μm emission from the inner 5 kpc of the active galaxy NGC 4258 with the SOFIA integral field spectrometer FIFI-LS. The emission is found to be associated with warm H2, distributed along and beyond the end of the southern jet, in a zone known to contain shock-excited optical filaments. It is also associated with soft X-ray hotspots, which are the counterparts of the “anomalous radio arms” of NGC 4258, and a 1 kpc long filament on the minor axis of the galaxy that contains young star clusters. Palomar CWI Hα integral field spectroscopy shows that the filament exhibits non-circular motions within NGC 4258. Many of the [C ii] profiles are very broad, with the greatest line width, 455 km s−1, observed at the position of the southern jet bow-shock. Abnormally high ratios of L([C ii])/L(FIR) and L([C ii])/L(PAH 7.7 μm) are found along and beyond the southern jet and in the X-ray hotspots. These are the same regions that exhibit unusually large intrinsic [C ii] line widths. This suggests that the [C ii] traces warm molecular gas in shocks and turbulence associated with the jet. We estimate that as much as 40% (3.8 × 1039 erg s−1) of the total [C ii] luminosity from the inner 5 kpc of NGC 4258 arises in shocks and turbulence (<1% bolometric luminosity from the active nucleus), the rest being consistent with [C ii] excitation associated with star formation. We propose that the highly inclined jet is colliding with, and being deflected around, dense irregularities in a thick disk, leading to significant energy dissipation over a wide area of the galaxy.