A strong area of low pressure combined with a warm front and favorable upper-level dynamics to produce 16 tornadoes across the region—14 in Minnesota and two in Wisconsin.

This supercell remained intact for approximately 150 miles (240 km) as it moved across the southern part of the state during the late-afternoon hours.

Gustavus Adolphus College in St. Peter was especially hard-hit, with several buildings damaged or destroyed, 2,000 trees lost, and nearly 80% of the windows on the campus shattered.

The driving force behind this tornado outbreak was a strong surface-based low-pressure area stationed over the western high plains.

On the morning of March 29, the low was centered over eastern Wyoming, with a warm front stretching eastward across Nebraska and Iowa.

A low-level jet from the south with winds of 50 knots (60 mph; 90 km/h) transported a plume of warm, humid air into the region, helping to push temperatures above 70 °F (21 °C) and dew points into the middle 60s °F (around 20 °C).

Five more tornadoes (all rated F2 or lower) briefly touched down during the next hour in the same general area; none of which inflicted major damage.

[3] On Saturday, March 28 at 11:30 am the Storm Prediction Center issued a Day 2 moderate risk of severe weather for southeast Minnesota, northeast Iowa, northwest Illinois and much of Wisconsin.

[10] Later model runs on March 28 only increased forecasters' confidence that a major severe-weather event would occur the following day.

[3] In the early-morning hours of Sunday March 29, forecasters at the Twin Cities NWS noticed that due to the model's prediction of strong wind shear and instability, the tornado risk was quite high for their region.

[3] Also on the morning of March 29, the Storm Prediction Center issued a Day 1 moderate risk of severe weather.

This moderate risk area was more narrow than the previous day's outlook, encompassing only southwest Wisconsin, northern Iowa and the southern third of Minnesota.

[3] Just before 12:00 pm, the Storm Prediction Center issued a mesoscale discussion stating that "[g]iven strength of vertical shear profiles, CAPE on the order of 2000 J/kg will support increasing potential for tornadic supercells during the afternoon hours, especially along an axis roughly from Yankton through Sioux Falls into Redwood Falls and Minneapolis/Rochester areas.

[9][34] At approximately 4:30 pm the twister, which witnesses described as a "mass of blowing dust" or "rolling fog bank"[9] entered Comfrey, a town of 550 people located in both Cottonwood and Brown Counties.

After traveling across six counties for 1 hour and 25 minutes and causing $75 million in damage,[33][36] the twister lifted back into the clouds at 5:15 pm 4 miles (6 km) southeast of Courtland.

[41] Gustavus Adolphus College, which sits on top of a hill on the west side of St. Peter, sustained heavy damage after taking a direct hit from the twister.

[38] Gustavus was on spring break at the time the tornado hit, so the campus was virtually vacant of students and there were no serious injuries or fatalities reported.

Debris from St. Peter that was sucked into the tornado fell back down to earth as far as Rice Lake, Wisconsin, over 130 miles (209 km) away.

[48] The half-mile (.8 km) wide tornado damaged several farms before hitting Le Center at F2 strength.

[48] Over the next hour, the supercell continued to track across southern Minnesota, dropping four more tornadoes in Rice and Dakota Counties.

[21][28][29] On April 1, 1998, seven counties in Minnesota were declared federal disaster areas: Brown, Le Sueur, Nicollet, Rice, Cottonwood, Blue Earth and Nobles.

[49] The money allotted from the federal government allowed the affected towns to clean up the damage and begin the rebuilding process.

[53] Three years after the tornado, the City of St. Peter reported that its population had grown by 2%; an unusual feat for a town that had so recently endured a natural disaster.

[43] After a summer of repairs, the symbolic end to the rebuilding process on campus occurred on October 22, 1998, when a new 175-foot (53 m) spire was placed atop the chapel.

[56] Following the tornado in Comfrey, residents were forced to temporarily evacuate the town due to several gas leaks,[41] and the Minnesota National Guard was called in to help secure the area.

Because the town's K–12 school was destroyed, students resumed classes two weeks later 20 miles (32 km) to the north in Sanborn.

[10] Because of above-average lead time for the warnings, and for excellence in forecasting the entire event, a bronze medal was issued to the Twin Cities NWS office the following December by the United States Department of Commerce.