At NR Junction (MP 111.3), where an MKT line once crossed at grade, the line to Topeka (used by Amtrak) departs to the northeast (with a speed limit of 30 mph through the junction in this direction) while the freight main continues due east. The Topeka line is single track, TWC, ABS, with a speed limit of 79-55 once the junction is cleared. It heads northeast from the wye, then turns east-northeast, north-northeast, and northeast again, past a detector at MP 104.6 and Lang, turns east-northeast past Reading (MP 96.55), northeast to Barclay, east and then north-northeast to the 5,000 ft. siding at Osage City (MP 84.3), where the speed limit is 50-40 briefly, a MoPac line once crossed at grade, and a Santa Fe branch once headed east.
The Topeka line continues due north, resuming the 79-55 speeds, past a detector at MP 82.3, turning east-northeast at the 3,400 ft. siding at Burlingame, where the speed limit is 60-55, briefly, and a Santa Fe branch from Manhattan once trailed in from the west. The line passes through Scranton (MP 71.6), turning northeast, east-northeast to Carbondale, whence a Kansas City, Wyandotte and Northwestern, later Kansas City Northwestern, once headed east to Lawrence, and north, with some curves back and forth, to Wakarusa, the 2,450 ft. siding at Pauline (MP 57.3), where the Seymour Industrial Spur leaves to the north-northeast, passes a location where a MoPac branch once ran below and another where that same branch trailed in one the west side of the line into the Kansas State capital, Topeka (MP 50.6), where the substantial brick depot is on the west side of the line, with the center of the city beyond it.
At BNSF Crossing (MP 50.2), a connector heads west to the former Rock Island line west to Herington, and another heads north across the Kansas River to the UP (and joint former Rock Island) line on the north side of the river (and once formed the ATSF line to Atchison), making a flat crossing with a connector from the Herington line, and the main line turns east on the southeast corner of the flat crossing, past the Santa Fe (now BNSF) Topeka Shops on the north side of the line, and then the Topeka Yard, also on the north side of the line, with yard tracks also on the south side of the line.
The line continues generally east, along the south bank of the Kansas River, past a grade crossing, a road bridge overhead, Intermediate Signals, a park alongside to the south, a bridge over a street, fields, the 7,900 ft. north side siding at Tecumseh (MP 46.0), two dirt road grade crossings, a spur southwest to the Kansas Power & Light Tecumseh Steam Plant, trailing in, another track trailing in from the southwest, extra track on the south side, a dirt road grade crossing in the fields, a cutting, a detector at MP 41.4, Spencer, and Grover, and turns east-southeast following the river, past a dirt track grade crossing, a cutting, a dirt track grade crossing, corn fields, a dirt track grade crossing, a bridge over a stream, an empty field, a gated dirt track grade crossing, an angled dirt track grade crossing, a dirt track grade crossing in the woods, a rocky cutting, a road bridge overhead, a slide fence on the south side, corn fields to the south, a dirt track grade crossing, a bridge over a stream, a gated dirt track grade crossing, Lecompton, a dirt road alongside to the south, a wooded cutting, a dirt road alongside to the south, ending at a farmyard, a dirt road grade crossing, a dirt track grade crossing, a dirt road grade crossing, a lake on the south side, a dirt track grade crossing, and the 2,500 ft. south side siding at Lakeview (MP 31.6), with a grade crossing within the siding.
There is a lake on the south side, a dirt road grade crossing, a dirt track grade crossing, cornfields to the south, and a dirt road alongside to the south, extra track on the south side, as the line turns south, past Intermediate Signals at MP 29.2, a dirt track grade crossing right at the signals, extra track on the south side, a spur west (on the south side) trailing in from the Kansas Power & Light Lawrence Station, dual road bridges overhead, a dirt track grade crossing, a bridge over a stream, a grade crossing, a bridge over a stream, a dirt road grade crossing in town (Lawrence), two road bridges overhead, a grade crossing west of the Amtrak station, which is on the east/north side, a grade crossing east of the station, and the 6,500 ft. east/north side siding at Lawrence (MP 26.5), where the speed limit falls from 79-55 to 35-30, there was once a flat crossing with the Kansas City, Wyandotte and Northwestern, later Kansas City Northwestern, and there is a seven track yard on the south/west side.
The line continues southeast, resuming the 79-55 speeds, past an angled grade crossing, a spur heading away into industry to the south, extra tracks on the south side, a spur trailing in from industry on the south side, a location where a Santa Fe branch once headed south, a spur trailing in on the south side, a grade crossing, a dirt road grade crossing, Intermediate Signals at MP 22.x, Nona, where the line turns east, corn fields to the south, a dirt road grade crossing, a detector at MP 21.8, a dirt road grade crossing, corn fields to the south, a dirt track grade crossing, a through truss bridge over a stream, a spur on the south side, heading away, a grade crossing, silos on the south side (no longer rail-served), and Intermediate Signals at Eudora, where the line turns east-northeast.
There are two dirt track grade crossings in the woods, a gated dirt road grade crossing, a rocky cutting, a bridge over drainage at MP 15.2, the Kansas River alongside to the north, a grade crossing, the river curves away, Intermediate Signals at Weaver, a dirt track grade crossing, a bridge over drainage, a grade crossing, a turn to the east again, a rocky cutting, a spur trailing in on the south side from the Sunflower Army Ammunition Plant, and the 8,600 ft. north side siding at DeSoto, and then north-northeast, still following the south bank of the Kansas River, past a dirt road grade crossing, Frisbie, an angled grade crossing, a road bridge overhead, Wilder, where it turns east and a branch from Leavenworth and Atchison once trailed in from the west (i.e., on the north side), a dirt track grade crossing, a dirt road grade crossing, a grade crossing, Chouteau, where it turns east-southeast, a road alongside to the south, a dirt track grade crossing, and a bridge over a stream, to the junction with the Freight Transcon at Holliday (MP 0.0/13.4), where it turns east northeast.