In the early 1850s The Leeds Northern (LNR), York, Newcastle and Berwick and York and North Midland railways were considering amalgamation, and in 1853 the M&DJR was admitted to that group of companies; and became part of joint traffic agreements. In 1854 an act of parliament allowing the YN&BR, LNR and Y&NMR companies to amalgamate into a new "North Eastern Railway" (NER) was passed; the association of M&DJR was formally announced at the first meeting of the NER, where, the distribution of income was decided to be based on traffic receipts over the next 5 years; the M&DJR obtained one director of a board of seventeen, and the company ceased to exist as an independent entity from 1 September 1854. In 1863 agreements relating to the merger of the Stockton and Darlington Railway (S&DR) set the Malton section's share of the combined company's profits at 0.29%, a sum which was not sufficient to meet running costs; the company attempted to renegotiate requesting a share of gross revenue, but were denied.