From the Oceanside Transit Center (MP 99.3), where the depot and Escondido trains' two tracks and stub island platform with umbrella sheds are on the east side of the main line to San Diego, the Escondido sub. heads south-southeast, along the east side of the main line, reduced to single track, CTC, speed limit 30 mph, past two grade crossings, CP Ocean (MP 99.5), where the speed limit rises to 55 mph, a grade crossing at the junction with the connector from the main line at CP Railroad (MP 100.1), where the speed limit drops to 25 mph for passenger trains and 15 mph for freight trains around the north leg of the wye as it turns from south-southeast to northeast, the passenger station (platform and umbrella shed on the north side of the line) at Coast Highway (MP 100.2), where the speed limit rises to 30-20, and the east apex of the wye at the east end of the platform, where the south leg trails in, at CP Wye (MP 100.3), with a grade crossing with Coast Highway also at the east end of the platform and an east-facing signal for CP Wye. Each station on this line has a set of signals facing the station, just off the end of the platform, providing the engineer with an indication of the current state of the signals on that section of the line before starting away when the conductor's signal is given.
There is an increase in the speed limit to 55-30 as the line turns east-northeast, past drainage alongside to the south, a grade crossing, I-5 bridging overhead, a grade crossing at Commerce Street, Intermediate Signals at MP 101.2, a grade crossing at State Tree Street, Oceanside Boulevard alongside to the north, the passenger station (platform and umbrella shed on the north side of the line) at Crouch Street (MP 101.5), a grade crossing with Crouch Street, Downs Street and then Skylark Drive alongside to the south, CP True (MP 102.6), formerly Talica, where the line expands to Two Main Tracks, CTC, a pedestrian crossing at the west end of the passenger station (two side platforms with umbrella sheds) at El Camino Real (MP 102.9), a pedestrian crossing at the east end, a grade crossing with El Camino Real, Alta Creek alongside to the north, and curves following the bends of the creek.
The line passes MP 103.5, a grade crossing at a driveway, Intermediate Signals at MP 103.x, the passenger station (two side platforms with umbrella sheds) at Rancho del Oro (MP 104.1), a pedestrian crossing at the east end of the platforms, a grade crossing at Rancho Drive, MP 104.5, a pedestrian crossing at the west end of the passenger station (two side platforms with umbrella sheds) at College Boulevard (MP 105.5), a pedestrian crossing at the east end, a grade crossing with College Boulevard, the end of Two Main Tracks in favor of single track, CTC, at CP School (MP 105.9), Falda, where the line turns northeast again, Intermediate Signals at MP 106.2, a grade crossing with Temple Heights Drive, a grade crossing, Intermediate Signals at MP 107.2, the passenger station (platform and umbrella shed to the north) at Melrose (MP 107.5), a grade crossing with divided Melrose Drive, where the speed limit is 45-25 on the clockwise curve to the south.
There is a grade crossing North Avenue, CP Angel (MP 108.0), where Two Main Tracks, CTC, start again and the speed limit is back to 55-30, a grade crossing with West Los Angeles Drive, Intermediate Signals at MP 108.4, a turn to the east, Intermediate Signals at MP 108.8, a turn to the south-southeast, MP 109.0, Santa Fe Avenue to the east, Olive Avenue to the west, and a pedestrian crossing at the east end of the passenger station (two side platforms with umbrella sheds) at the Vista Transit Center (MP 109.2), followed by grade crossings with divided Vista Way and divided Broadway.
The line heads south, past a grade crossing with Lado de Guajome Street, with a jog southeast, where the speed limit is 25-20 for the curves, before continuing south, past a grade crossing with Escondido Avenue, the passenger station (two side platforms with umbrella sheds) at Escondido Avenue (MP 110.1), and a pedestrian crossing at the south end of the station, followed by a turn curvily east, with the speed limit dropping to 30-25, on an embankment, becoming a ledge with the valley to the north, past Intermediate Signals at MP 110.8, and then curvily southeast past a grade crossing at Mar Vista Drive, CP Avenue (MP 111.4), where single track, CTC, resumes and the speed limit is 50-30, with Hannalei Drive to the west, an angled grade crossing with Santa Fe Drive, which had been alongside to the east, and now runs to the west, and a turn east past a rade crossing at Buena Creek Road and the passenger station (platform with umbrella shed to the north) at Buena Creek (MP 112.4).
There is a bridge over drainage, and a turn to the south again, as the speed limit returns to 55-30, past a grade crossing with Estrelita Drive, Mission Road alongside to the west, a turn east-southeast, a speed limit of 40-30, a turn to the south, with a road bridge overhead, and then south-southeast, MP 113.5, Intermediate Signals at MP 113."2" , Mission Road alongside to the southwest again, turning across a grade crossing, and then running alongside to the northeast, the resumption of Two Main Tracks, CTC, at CP Missy (MP 114.5), a grade crossing with Las Posas Road, a turn to the east-southeast, with Mission Road remaining alongside, a spur on the south side, MP 115.0, the passenger station (two side platforms with umbrella sheds) at Palomar College (MP 115.1), with the college across Mission Road to the north, a pedestrian crossing east of the platforms, MP 115.5, a grade crossing at Knoll Road, Intermediate Signals at MP 115."2", Autumn Drive alongside to the south, a grade crossing with Pico Avenue, a road bridge carrying Twin Oaks Valley Road overhead, the passenger station (two side platforms with umbrella sheds) at San Marcos Civic Center (MP 116.4), and a grade crossing with San Marcos Boulevard.
The San Marcos Bypass Freight Track (single track, CTC, speed limit 30-25) diverges to the east-northeast, just east of the station, at CP Loopwest (MP 116.5 on Track 1), where the passenger speed limit drops to 25 mph for the passage through the campus of Cal State San Marcos, turning south past a bridge over drainage, an embankment, a bridge over the SR 73 freeway, a turn to the east, on viaduct, bridging over a street on the curve to the Cal State San Marcos passenger station (island platform with umbrella shed) at MP 117.2, which bridges over a north-south street within the station, with a pedestrian crossing at the east end of the station and a street alongside to the south, after which the passenger speed limit rises to 45 mph as the line turns east past MP 117.5 and CP Shelly (MP 117.7), where it reverts to single track, CTC, bridging over SR 73 again, then a street and a bikepath, and descending to CP Loopeast (MP 118.4), where the freight track trails back in from the west-northwest, the speed limit becomes 45-30, and the line turns curvily east-southeast.
The line passes MP 118.5, where the speed limit rises to 55-30, with Mission Road alongside to the north, a grade crossing with Rancheros Drive, a bridge carrying SR 73 overhead, a grade crossing with Barham Drive, the passenger station (north side platform with umbrella shed) at Nordahl (MP 119.2), a grade crossing with Nordahl Road, MP 119.5, a grade crossing with Enterprise Street, a spur on the south side to industry, a grade crossing with Andreasen Drive, CP Holdout (MP 120.4), a grade crossing, dual road bridges carrying I-15 overhead, a spur on the south side, a grade crossing with Hale Avenue, the storage tracks on the north side start (where a wye on the north side used to be), a grade crossing with Railroad Avenue, a bridge over drainage, CP Yard (MP 121.1), as the line turns southeast, the speed limit drops to 30-15, and the passenger station (center stub platform with tracks on each side) at Escondido Transit Center (MP 121.3), which is as far as the passenger trains go, a grade crossing with Valley Parkway, and CP Avo, at its southeast end (also MP 121.3), where Yard Limits begin (for the freight trains) and the speed limit drops to 10 mph for the rest of the way to the End of Track (MP 121.6).