In 1921, the Western Pacific built its 23-mile San Jose Branch, which begins east of Niles Junction and continues south through Milpitas toward San Jose. The Niles-to-Milpitas section was abandoned earlier this decade after a derailment just north of the Milpitas Yard. A connector track was built to the parallel ex-SP Milpitas Line (currently the UP Warm Springs Sub) instead of rebuilding the track.
A small section of the abandoned right-of-way will be used in the Warm Springs Sub's new grade separation project in Fremont. Another portion of the line is being converted into a trail.