The prospect of a nuclear-capable Islamic Republic of Iran has for several decades been a serious international concern, especially for the United States and its close allies. The problem (if there is one) is one of an intensely political nature, and is grounded ultimately in deep-seated ideological differences between nations and cultures. In this short review, I will attempt to contextualize the current situation and give a brief analysis of what may happen if Iran acquires advanced nuclear capabilities.
The Iranian nuclear program began in the mid-1950s, with the encouragement and blessings of the Eisenhower and Ford administrations.  The government of the reigning monarch at the time, Mohammed Reza Shah, signed and ratified the Nuclear Nonproliferation Treaty (NPT) in 1968 and agreed to International Atomic Energy Agency safeguards soon afterwards.  By 1976, Iran had received a small research reactor, a complete nuclear fuel-cycle, and considerable foreign assistance in developing a 20MW light-water reactor and associated power grid.  The development of nuclear power in Iran was a highly publicized process, and the Shah had a stated goal of generating 2000MW of nuclear power for civilian use by the beginning of the new millennium. 
The Iranian Revolution of 1979 signaled a radical departure from what had been a well documented, regulated, and internationally sanctioned path towards nuclear energy capabilities. [1,2] Although the United States had begun to grow wary of Iranian nuclear ambitions as early as 1974, American support for the Iranian program stayed relatively steady.  However, after the 1979 revolution, almost all foreign nuclear assistance was cut entirely. The Iranian nuclear program was abandoned for several years, and resurrected in the late 1980s for reasons that remain unclear. 
The current political climate in Tehran involves a bewildering mix of religious ideology and secular political calculation. The two most prominent Iranian political figures, Supreme Leader Ali Hussein Khameini and President Mahmoud Ahmadinejad, offer different political and religious agendas, which make the interpretation of Iranian policies very difficult - especially with respect to nuclear issues. Since the rebirth of the Iranian nuclear program in the late 1980s, several top Iranian officials have stated that Iran seeks only to enrich fuel for research and power reactors. [1,4] Indeed, a 2003 IAEA report concluded that Iran's nuclear program was not military in nature and had no weapons applications.  However, by 2006 the IAEA had reversed its position towards Iran and passed a series of increasingly stricter resolutions that culminated with a report to the United Nations Security Council. [1,5] This shift seems to have been largely in response to pressure from the United States, in addition to the fiery rhetoric of the newly elected President Ahmadinejad. It is worth noting that the IAEA does not object to an Iranian nuclear program in itself, but rather to the weaponization of its technology - indeed, a 2007 resolution reaffirms Iran's "inalienable" right to nuclear energy. 
The current situation (and the source of the 2000+ New York Times articles on the topic) revolves around Iran's continued enrichment activities and the development of full fuel-cycle capabilities. As of 2011, Iran has at least 3,000 kg of 3.5% enriched uranium, with the capacity to enrich to at least 18.5%.  The regime recently announced plans to install 3,000 new advanced centrifuges at its enrichment facility in Natanz, in defiance of pressure to curb its fuel cycle activities.  Interpreting the nuclear ambitions of Iran is incredibly difficult; the Republic's leaders repeatedly affirm that they have no intentions to develop nuclear weapons while at the same time ignoring IAEA resolutions and expanding their centrifuge fleet. Likewise, many western nations (including the United States) are unwilling to cogently articulate why Iran should be required to curtail its nuclear pursuits. In light of this apparent lack of transparency, it may be helpful to examine critically the worst-case scenario that frightens so many western nations: the development by Iran of a deliverable nuclear weapon.
What will happen if Iran acquires a nuclear weapon? It is obviously impossible to divine the future with any certainty, but we may critically examine the options and their implications. There are two basic scenarios that we use as a framework for this discussion; the first is that Iran uses its nuclear weapon, and the second is that it does not.
In the scenario that Iran uses a nuclear weapon in a first-strike operation, it is likely that the targets would be Israel or the United States.  In either case, retaliation by the United States would likely be swift and heavy-handed - in a 2008 campaign speech, then-Senator Hillary Rodham Clinton stated that the United States "would totally obliterate" Iran in the event of an attack. Given this probable outcome, a nuclear strike by Iran would indicate that the Iranian government values its regional and global political goals over the lives of many thousands of its citizens. This is likely not the case; in the 33 years since the revolution, most actions by the Iranian state (inflammatory rhetoric aside) have been rational and calculated for the long-term persistence of the current Islamic regime. [1,9] However, if past nuclear near-confrontations have taught us anything, it is that rational administrations can arrive at irrational decisions. One has only to recall the close calls of the Cold War for this to be clear.
More likely than a pre-emptive nuclear strike is a scenario in which Iran postures its nuclear weapon as a deterrent against the United States. In this case, there are several important points to consider. The first is the risk of proliferation of nuclear material or information - Iran is already a proliferation concern for the IAEA and the UN. [5,6] The second closely related concern is Iran's reputed connections to several active terrorist organizations. Perhaps most important is the inevitable destabilizing effects a nuclear Iranian state will have on one of the most volatile regions of the globe. [1,3,7,8] In the event that Iran obtains a nuclear weapon, it is likely that the greatest threat will not come from Iran itself. The problems will rather lie in the possibility of a destabilizing arms race in the Middle East, an emboldened cadre of terrorist organizations that consider themselves under Iran's nuclear-reinforced protective umbrella, and the risk of nuclear technologies falling into the hands of those uninhibited by ethical concerns.
Both the United States and Israel have effectively made clear that they will not tolerate a nuclear Iran. The rhetoric that surrounds this issue is thick and difficult to pierce, and is issued both by Iran and the states opposed to its nuclear activity. Because of this, it is nearly impossible to know for certain the capacity of the Iranian nuclear program or the lengths to which countries like the United States will go to reduce it. Hopefully we can rely on the powers of collective reason to guide us through this delicate and complicated nuclear landscape.
© Daniel Perret. The author grants permission to copy, distribute and display this work in unaltered form, with attribution to the author, for noncommercial purposes only. All other rights, including commercial rights, are reserved to the author.
 J. Amuzegar, "Nuclear Iran: Perils and Prospects," Middle East Policy 13, 90 (2006).
 C. Kurzman, "Structural Opportunity and Perceived opportunity in Social-Movement Theory: The Iranian Revolution of 1979," American Sociological Review 61, 153 (1996).
 "Prospects for Further Proliferation of Nuclear Weapons," U.S. Central Intelligence Agency, Special National Intelligence Estimate SNIE 4-1-74 August 1974. [This is a censored, declassified version of a secret report.]
 J. Zarif, " We Do not Have a Nuclear Weapons Program," New York Times, 6 Apr 06.
 "Resolution 1737 (2006)," United Nations Security Council, S/RES/1737(2006), December 2006.
 "Resolution 1747 (2007)," United Nations Security Council, S/RES/1747 (2006), March 2007.
 "Iran's Nuclear Program: Status and Breakout Timing," The Bipartisan Policy Center, September 2011.
 "Iran Says 3,000 Centrifuges Being Built," New York Times, 3 Mar 13.
 M. Rubin, "Can a Nuclear Iran Be Contained or Deterred?" American Enterprise Institute, November 2008.