We present a sub-100 pc-scale analysis of the CO molecular gas emission and kinematics of the gravitational lens system SDP.81 at redshift 3.042 using Atacama Large Millimetre/submillimetre Array ( ALMA ) science verification data and a visibility-plane lens reconstruction technique . We find clear evidence for an excitation dependent structure in the unlensed molecular gas distribution , with emission in CO ( 5-4 ) being significantly more diffuse and structured than in CO ( 8-7 ) . The intrinsic line luminosity ratio is r _ { 8 - 7 / 5 - 4 } = 0.30 \pm 0.04 , which is consistent with other low-excitation starbursts at z \sim 3 . An analysis of the velocity-fields shows evidence for a star-forming disk with multiple velocity components that is consistent with a merger/post-coalescence merger scenario , and a dynamical mass of M ( < 1.56 kpc ) = 1.6 \pm 0.6 \times 10 ^ { 10 } M _ { \odot } . Source reconstructions from ALMA and the Hubble Space Telescope show that the stellar component is offset from the molecular gas and dust components . Together with Karl G. Jansky Very Large Array CO ( 1-0 ) data , they provide corroborative evidence for a complex \sim 2 kpc-scale starburst that is embedded within a larger \sim 15 kpc structure .