The New Brunswick, Millburn and Orange Railroad was proposed as a connection between the two, allowing for a C&A route to Jersey City without using the NJRR.

Because of this, the HL&I decided to help the M&E by building their new alignment, using the New York and Erie Railroad's Long Dock Tunnel.

To use the Erie's tunnel a supplement to their charter was needed; this was passed March 8, 1860 after arguments against the bill from the NJRR.

On November 1, 1865, the Atlantic and Great Western Railway leased the M&E as part of its planned route to the west.

It was later extended much further east toward Paterson and then south to return to the main line at the west end of Bergen Hill; this opened on September 17, 1870.

A realignment was later built at the west end, bypassing Denville and some curves, for a shortcut of both the branch and the main line.

The Harrison Cut-off was built in the 1920s[5] as a connection from the Boonton Branch at Kingsland south to the main line in Kearny.

The Morris and Essex Extension Railroad was chartered in 1889 and opened later that year, connecting the Boonton Branch to Paterson.

The Passaic and Delaware Extension Railroad was chartered in 1890 and opened later that year, extending the line to Gladstone.