For the second time in three days, the vast majority of South Central Nebraska was spared severe thunderstorms, while a more significant severe weather event unfolded barely off to the south and east on this Thursday, primarily within central/northeast Kansas. Within the 24-county South Central Nebraska area, there were only a few strong to marginally severe storms that dropped hail mainly in the far southeast counties of Thayer and Fillmore, including stones up to half dollar size near Gilead.
Similar to the convective event a few days prior on the 4th, this one consisted of two primary rounds of activity. The first round focused mainly between 10 a.m. and 12:30 p.m. CDT as a smattering of elevated storms flared up over Nuckolls and Thayer counties, then gradually drifted northeast through parts of Clay, Fillmore and York counties before exiting the local area into eastern Nebraska. While most of these cells remained below severe limits, one prompted a radar-indicated Severe Thunderstorm Warning for Fillmore County that yielded a report of nickel size hail near Grafton. These elevated storms developed in classic fashion a few counties to the north-northwest of a well-defined surface warm front stretched from central Kansas into far southeast Nebraska.
Following the departure of the first round, there was a several-hours lull in noteworthy activity within South Central Nebraska as most counties saw only isolated to scattered showers and weak, non-severe thunderstorms between 12:30-4:00 p.m. CDT. Meanwhile, the aforementioned warm front draped near the far southeast corner of the local area (that the early convection focused north of) started surging south-southeast as an increasingly-well-defined cold front, marked by north winds gusting 25-35 MPH and dewpoints falling into the 30s/40s F. By 3-4 p.m. CDT, this front had barely cleared South Central Nebraska to the southeast. As it turned out, this frontal timing ended up being a fortunate break for the local area. This was because from 3-6 p.m. CDT, a broken line of supercell storms erupted along the front over northeast Kansas and gradually morphed into a squall line, yielding several reports of Sunflower State severe weather, including tornadoes. However, a tiny fraction of South Central Nebraska, specifically the southeast edges of Thayer County, did not escape unscathed. This was because the left-split of a supercell that initiated over Cloud County KS rapidly ejected north-northeast across the state line between 4-5 p.m. CDT, essentially riding up the Thayer-Jefferson County line. On the Thayer County side, dime to half dollar size hail was reported in rural areas near Gilead before the storm departed into eastern Nebraska, signaling an end to all South Central Nebraska convection for the day.
Turning to the day's meteorological setup, the aforementioned surface frontal timing/position was the primary factor in sparing South Central Nebraska from a more significant severe weather threat. In the mid-upper levels, a potent shortwave disturbance embedded within a larger-scale trough ejected eastward into the Central Plains over the course of the day. Despite all convection over the local area being elevated in nature, hail production in far southeast counties was supported by as much as 1000-2000 J/kg most-unstable CAPE in the presence of strong deep-layer wind shear around 60 knots.

Hail in FILLMORE, NEBRASKA
From 06-OCT-16 10:35:00 to 06-OCT-16 10:35:00 (CST-6)
Location: GRAFTON
Magnitude: 0.88 
Property damage: 0.00K
Crop damage: 0.00K
Reported by: Trained Spotter

Hail in THAYER, NEBRASKA
From 06-OCT-16 15:21:00 to 06-OCT-16 15:21:00 (CST-6)
Location: HUBBELL
Magnitude: 1.25 
Property damage: 0.00K
Crop damage: 0.00K
Reported by: Trained Spotter

Hail in THAYER, NEBRASKA
From 06-OCT-16 15:33:00 to 06-OCT-16 15:33:00 (CST-6)
Location: GILEAD
Magnitude: 0.75 
Property damage: 0.00K
Crop damage: 0.00K
Reported by: Trained Spotter