We assemble a catalogue of Magellanic Cloud red giants from Data Release 2 of the $Gaia$ mission and, utilising machine learning methods, obtain photometric metallicity estimates for them. In doing so, we are able to chemically map the entirety of the Magellanic System at once. Our high resolution maps reveal a plethora of substructure, with the Large Magellanic Cloud (LMC) bar and spiral arm being readily apparent. We uncover a curious spiral-like feature in the southern portion of the LMC disc, hosting relatively metal-rich giants and likely a by-product of historic encounter with the Small Magellanic Cloud (SMC). Modelling the LMC as an inclined thin disc, we find a shallow metallicity gradient of $-0.048\pm 0.001$ dex/kpc out to $\sim 12\circ$ from the centre of the dwarf. We see evidence that the Small Magellanic Cloud is disrupting, with its outer iso-density contours displaying the S-shape symptomatic of tidal stripping. On studying the proper motions of the SMC giants, we observe a population of them being violently dragged towards the larger Cloud. The perturbed stars predominately lie in front of the SMC, and we interpret that they exist as a tidal tail of the dwarf, trailing in its motion and undergoing severe disruption from the LMC. We find the metallicity structure in the Magellanic Bridge region to be complex, with evidence for a composite nature in this stellar population, consisting of both LMC and SMC debris.