It does not appear to be clear that President Obama and his administration understand all the implications that allowing Iran to acquire a nuclear weapon would entail. For there are many that could essentially transform the Middle East.
One of the unintended consequences of allowing this to occur would be the growth of nuclear proliferation in the Middle East. The first nation that can be expected to pursue nuclear weapons is Saudi Arabia. Considering its proximity to Iran and that it is made primarily of Sunni Muslims, they would most likely want to offset the "Shia bomb" of Iran. This could happen also due to the fact that of Iran acquired a bomb it will feel emboldened and could try to pressure the surrounding Gulf states into following its will possibly vis-a-vis oil. This would only make sense to protect their interests.
From there it could be a domino effect. Considering Iran had one and Saudi Arabia was working on acquiring one the bigger nations in the region could also see it as only being their prerogative that they have one as well. These nations could include Egypt, Turkey, and possibly Syria. If all these nations were to acquire nuclear weapons you would see a dramatically different Middle East, one where an arms race has transformed it into a nuclear hotbed.
In addition to the threat of nuclear proliferation, Iran's acquisition of a nuclear weapon poses an existential threat to Israel. There is no question in the mind of the Israeli leadership that they can risk that Ahmedinejad is posturing for his domestic base. They cannot risk a nation such as Iran acquiring such a capability and either directly threatening it or passing it off to a terrorist organization such as Hezbollah or Hamas. President Obama does not seem to understand this position of Israel, which in and of itself is disconcerting. If Israel feels Iran is close to acquiring the bomb it, without a doubt, will take action. This should be allowed.
These are only two of the most obvious consequences that the administration is not willing to face for one reason or another. They cannot simply submit to the inevitability of it and give up and in the process abandon allies such as Israel most importantly, and others in the region such as Saudi Arabia and the Gulf states.
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