In the spring of 2013, TWISTEX was conducting lightning research (including with a high-speed camera) when active tornadic periods ensued in mid to late May, so Samaras decided to deploy atmospheric pressure probes and to test infrasound tornado sensors that were still under development. At 6:23 p.m. on May 31, 2013, Samaras, his 24-year-old son Paul (a photographer), and TWISTEX team member Carl Young (a meteorologist), 45, were killed by a violent wedge tornado with winds of 295 mph (475 km/h) near the Regional Airport of El Reno, Oklahoma. The TWISTEX vehicle was struck by a subvortex, which generate the highest winds and some of which were moving at 175 mph (282 km/h) within the parent tornado. Their Chevrolet Cobalt was distinguishable as a vehicle to the first responding sheriff's deputy only due to its single intact wheel, as it had been compressed into a ball of metal after the tornado tumbled it approximately one-half mile (0.8 km).
Samaras is survived by his wife Kathy, two daughters, a son from a previous relationship, brothers Jim and Jack, and two grandchildren. His memorial service was held on June 6, 2013 at Mission Hills Church in Littleton, Colorado.