Mobile Ave was essentially a backdoor portal into and out of the matrixs system that was controlled by the exiles, namely the Merovingian. In fact it was probably the only access point that wasnt controlled by either the humans nor the machines. When Neo first remote accessed control over the sentinels, and afterwards fell unconscious, his mind was essentially jacked into the matrix. However this time he wasnt using a secured access point that was controlled by the humans. My guess is that he unknowingly was able to do this by forcing a connection through Mobile Ave. This could have been made possible simply through his introductions to and interactions with the Merovingian and the Architect, similar to how pairing up your smart phone to your car via Bluetooth, gives your car access to various functions and folders within your phone. By meeting the Architect and coming as close to the source as possible without actually returning to it, Neos coding gained access to a higher level of control over both the matrix and the machines. By meeting the Merovingian and experiencing his control over portals within the Matrix, Neo may have also gained access to some of the functions and programs that the Merovingian had control over. Kissing his wife Persephone in the bathroom may have even helped forge this connection.