At the crossovers and junction at Fremont (MP 39.2), the 3MT, CTC, 30 mph, direct line (former C&NW) to Missouri Valley, turns away on the north side from the 2MT, CTC, 40 mph, original UP Omaha line continuing southeast on the south side, turning south-southeast past four tracks to the south, a grade crossing, an eight-track yard to the south, extra track to the north, to shuttle-enable grain elevators, a closed grade crossing, a grade crossing, Intermediate Signals, a road alongside to the north, Intermediate Signals, crossovers at Mercer (MP 34.1), where the speed limit has increased to 70 mph, and the line becomes Double Track, Automatic Block Signals, an east-facing spur from silos to the south, Intermediate Signals, a bridge over a stream, a road alongside to the north, two grade crossings at driveways, a grade crossing, a dirt track grade crossing, a spur from elevators to the south, trailing in, a road bridge overhead, and three extra tracks to the south.
There is a turn to the southeast past the wye junction on the southwest side with the UP Lincoln sub. heading southwest at Valley (MP 28.0), where there is a 4,533 ft. south side siding and a 6,356 ft. north side siding, a grade crossing, two extra tracks to the south, a road bridge overhead, Intermediate Signals, a road to the north, a grade crossing, a Westward Hold Signal at MP 26.1, a road bridge overhead, a grade crossing, Intermediate Signals and a spur at Waterloo (MP 24.7), streets to the north and south, and Intermediate Signals, east to the 3,654 ft. center siding at Elkhorn (MP 21.6), a bridge over a stream, a grade crossing, a road bridge overhead, two bridges over drainage, and a through-girder bridge over a stream, just south of due east past detectors at MP 20.0, a grade crossing, a road alongside to the south, and a dirt road grade crossing, and south-southeast past an east-facing south-side spur for industry, crossovers at Pacific Street (MP 17.4), where 2MT, CTC, resume, a road alongside to the south, a through-girder bridge over a street, and the junction with the Millard Industrial Lead on the south side at Lane (MP 16.7), where the speed limit is 50 mph.
The line turns east, past a divided street to the south, a road bridge overhead, Weco (MP 13.6), where the speed limit is back to 70 mph, two extra tracks to the south, a spur at Nasco (MP 12.2), an embankment, dual road bridges overhead, Woody (MP 11.1), a road bridge overhead, 95th Street (MP 10.9), an Interstate to the north, detectors at MP 10.0, extra track to the south, a bridge over a divided street, embankment, Intermediate Signals at MP 9.12, Seymour (MP 8.9), a spur to industry on the south side, a road bridge overhead, a six-track yard to the south, serving industry, a bridge over a stream, a bridge over the erstwhile MoPac line to Webster Street, embankment, a through-truss bridge over the erstwhile Chicago & Northwestern line to South Omaha, and a bridge over a divided road.
There are crossovers at 57th Street (MP 7.7), embankment, a bridge over a road, the junction with the line on the south side to South Omaha and the west leg of the Wimmer Wye at 48th Street (MP 6.9), where the line turns just north of due east, and then east again, a bridge over another erstwhile MoPac line at Elevator, dual road bridges overhead, and a turn north-northeast at Summit (MP 5.1), where the speed limit has fallen to 40 mph and the east leg of the Wimmer Wye trails in on the south side, past a road bridge overhead, a through-truss bridge over a stream, and a road bridge overhead, as the BNSF line from Lincoln, also used by Amtrak, comes alongside to the southeast.
The line passes beneath the spaghetti junction (seven road bridges overhead) of I-80 and I-480, and passes the crossovers and yard at 20th Street, Omaha (MP 3.8), turning northeast, with the BNSF line remaining alongside to the southeast, past Tower C, on the southeast side, a road bridge overhead, the crossovers and (former) junction, with an erstwhile connector northeast to the MoPac at Webster Street, at 16th Street, aka Tower B (MP 3.4), two road bridges overhead, three extra tracks to the south, a bridge voer a street, an angled bridge carrying 13th Street overhead, and two bridges over streets, turning east past another road bridge overhead at 10th Street, right at the erstwhile Union Station (the building is now The Durham Western Heritage Museum) on the north side, with a single track on the north side of the line adjacent to the building, from 16th Street to 7th Street, and the former location of an erstwhile intermodal yard on the north side.
Another road bridge crosses overhead, there is a jog east-southeast and east again, a bridge over a street, the crossovers and junction with the connector on the south side, coming east from the BNSF line, at 7th Street (MP 2.5), where the station track also connects back in, West Missouri River Bridge (MP 2.4), where the speed limit has dropped to 25 mph, the five-span through-truss bridge over a line along the west bank of the river, and the Missouri River, from Nebraska to Iowa, a road passing below on the east-bank levee, and East Missouri River Bridge (MP 2.1).
There are crossovers at CP B002 (MP 2.0), where 3MT, CTC, start, a bridge carrying I-29 overhead (or carrying the line over I-29), crossovers and three sets of yard tracks heading southeast at Council Bluffs (MP 0.9 - MP 0.6), at the east end of which the 3MT become 2MT and turn east-northeast, with speed limit 20 mph, as another set of yard tracks continues east, MP 0.0=MP 351.7 as the original UP becomes the former C&NW, with Pool Yard alongside to the south, and the junction with the BNSF (former CB&Q) line to Pacific Junction, heading just south of due east at BN Junction (MP 351.3), where CTC gives way to Yard Limits and the main line turns northeast.