"Jughead" was a hydrogen bomb that the US Army failed to detonate while trying to obliterate all traces of Communism. Nuclear testing in the Pacific Islands had become an essential part of American culture and the general theory was that most islander nations were Communist or Japan and that if they were hit, it was probably God's way. Richard Alpert, upon noticing that there was a now a radioactive bomb on his island, expressed feelings that maybe the island had been mistaken for Vietnam. Unfortunately, that was not the case.
When initially appearing in 1954, Daniel Faraday demanded that Jughead be buried. In actuality though, Faraday mumbled quizzically and sought for the right words trying to convey this message to the Native and Ellie sort of inferred what he might be asking.
23 years later, Faraday refuted his claims that radioactivity was a bad thing and designed a plan that was constituted on the idea that setting off an atomic bomb would magically reset the universe. Faraday miscalculated, however, and so it turned out that detonating a 20 ton hydrogen bomb actually just kills people.