From SJ Junction/Topeka (MP 68.2), where the former Rock Island line from the south trails into the double track UP Kansas sub. (and once continued north as the Rock Island line to St. Joseph), and there is a yard, the line heads east, Two Main Tracks, CTC, with speed limit 30 mph, turning just east of due north, past crossovers at East Topeka (MP 67.4), where a connection from the former Santa Fe in downtown Topeka trails in on the east side (and once continued across the line on the way to Atchison), and then east, away from the former Santa Fe right-of-way, and along the north side of the Kansas River, past detectors at MP 61.3, Grantville (MP 61.0), where Double Track, Automatic Block Signals, replace the 2MT, CTC, and the speed limit has risen to 70 mph, Newman (MP 55.9), a Westward Hold Signal at Medina (MP 54.0), and an Eastward Hold Signal at MP 52.3, the 6,305 ft. center siding at Perry (MP 51.6).
The line edges just south of due east, following the general course of the river, past Williamstown, detectors at MP 46.8, and Buck Creek, turning southeast past Midland (MP 43.3), south (and getting closer to the north bank of the river) past an Eastward Hold Signal at MP 40.0, where the speed limit is 40 mph and the 2,299 ft. center siding at Lawrence (MP 38.2), where the erstwhile Kansas City, Wyandotte & Northwestern once headed south (i.e. on the west side), across the river, and the line turns east, following the general course of the river valley, past Bismark Grove, and Turkey Creek (MP 37.7), where the speed limit has returned to 70 mph and the KCWN line to Leavenworth once left on the north side, east-southeast past a former crossing with the erstwhile Kansas City, Kaw Valley & Western (which then followed the UP line on its north side all the way to Kaw Junction), east-northeast past Fall Leaf and detectors at MP 31.6 to the 8,810 ft. south side siding at Linwood (MP 30.1 - MP 28.1), where there are crossovers and 2MT, CTC, replace the DT, ABS, east past Lenape and Coldspur, and then northeast.
There are crossovers at Loring (MP 21.0), where the speed limit has fallen to 60 mph and the line turns north-northeast, still following the river, a former crossing with an erstwhile Santa Fe line between Holliday and Leavenworth, Bonners Springs (MP 17.5), where the speed limit has fallen to 55 mph as the line turns northeast, Sunflower (MP 16.7), as it turns east, a detector at MP 15.6, where the speed limit has returned to 70 mph, Forest Lake, Edwardsville (MP 13.9), and Miller (MP 12.8), where the line turns east-northeast, and then northeast, crossovers at CP Z010 (MP 10.0), crossovers and a 4,975 ft. south side siding off Track 2 at Muncie (MP 9.4 - MP 8.4), and crossovers at West Yard (MP 6.4), where the line curves around to just south of due east, the speed limit falls to 40 mph and the Kansas sub. starts to overlap with the UP Kansas City terminal sub.