The natural assumption is that the end game for Iran's nuclear energy efforts is an atomic bomb sitting on top of a long-range ballistic missile, but intelligence agencies secretly think that may not be the case. According to The Los Angeles Times, national intelligence estimates from as recently as last year, say that Iran stopped trying to actively build a nuclear weapon in 2003 and has no plans to do so at the moment.
If that were true it would mean taking Tehran at its word when its leaders say they want to use nuclear energy for peaceful purposes only. Taking the Ayatollah at his word, however, is not something Israelis and many American leaders are inclined to do. The chairman of the House Intelligence Committee (who has presumably seen these reports) has stated outright that the country is pursuing nuclear weapons. And just because they aren't building one right now, does mean they can't change direction. Once you master the secrets of nuclear energy, turning that knowledge into weapons is not a huge leap. Nuclear inspector David Albright says it would only take six months for Iran to use its centrifuges to create bomb material, should they change their minds.