Whalen was among a group of volunteer first responders who aided in the recovery after the Battle of New York. He and fellow firefighters found a Chitauri Helmet that they kept as souvenir.
Unbeknownst to them, the helmet carried a virus which causes those who contract the virus to die in a very strange way. Months after, Whalen, Adam Cross and Tony Diaz decided to polish the helmet. Whalen contracted the virus.
Frank Whalen succumbed to the virus while in his barn. He had locked the barn doors and had a shotgun with him, which Phil Coulson initially supposed was for protection against someone trying to attack Whalen. It is unclear whether Whalen also thought he would be attacked or if he was going to shoot himself to stop the "humming" symptom of the virus. After the virus killed Whalen, it caused his body to float in the air.
Leo Fitz used one of the D.W.A.R.F.s to cause a static electricity spark, which caused Whalen to fall straight into a coffin set up to catch him.
Whalen's body was brought on board the Bus to be investigated by Jemma Simmons. Simmons determined after examining Whalen's brain that he was not killed by a person, but a virus.