Has the Supreme Leader Ever Been Challenged? part 1
The Supreme Leadership in the Islamic Republic Regime: Why & How!
The infrastructure in place, in the IR system, for selecting the Supreme Leader was only fully implemented after the death of Khomeini with the purpose to safely sustain the regime during Supreme Leader transitions. Two councils which have the duty to “approve” and “counsel” the Supreme leader were only established after Khamenei. These councils technically have the power to impeach the Supreme Leader, however this is impossible for all practical purposes.
1) Those who have made it to the top of this pyramid and have a position on these councils, have been filtered enough to never pose such a threat.
2) Should they somehow get that far in the system and change their mind, their life is literally in danger.
3) The SL, himself, has the power to appoint members to these councils. Clearly, it is not in his interest to appoint members who will oppose him.
Who dare speak against the king?
The closest semblance of a threat to the Supreme Leadership’s (Khameneie’s) power in the recent decade, came during the last presidential elections (2005) between Ayatollah Rafsanjani and Ahamadinejad. In the fiasco those elections were, Ayatollah Ali-Akbar Hashemi Rafsanjani pioneered public dissent , of sorts but it was dissent anyhow, against the Supreme Leadership by a high-cleric who was himself born and fed by the Regime (!).
(1989-1997)
As a short introduction, Rafsanjani served as president of the Islamic Republic from 1989-1997. He was president during the hardest times Iranians experienced after the revolution. Rebuilding the nation after it went through a revolution and a war was a daunting task. Rafsanjani’s economic policies and proposals are actually noteworthy. At the time, he may have been the only and the best candidate the regime would approve to do the job. (Economists, such as Isfahani, as well as news media acknowledge this.)
As far as civil rights and political repression is concerned, Rafsanjani upheld the ideals of the Revolution quite well—unfortunately. He and his family also made corrupt economic transactions and investments. The Rafsanjani family today is one of the wealthiest families in Iran. It is worth mentioning that, of all the thieving characters this regime has seen, credit should be given to the Rafsanjanis because they seem to be one of the few who do actually invest in Iran. Their investments do maintain and better the lives of citizens and do complement to urbanization projects throughout Iran.
Again, I am not advocating Rafsanjani’s sainthood, nor am I turning a blind eye to his faults/disservice … However, the case still stands that Rafsanjani seems to be the most influential regime authority with the greatest leverage who has, and most certainly, can rise in some sort of dissent while keeping his life safe.
(2005 Elections)
Rafsanjani had an obvious lead in the first round of elections. At this time, he repeatedly emphasized, via his press conferences, the close relationship he had with Khomeini in the 70s. He would use this as a justification for his new policy proposals–some of which seemed to question Revolutionary Ideals greatly. Rafsanjani who, in my opinion, is quite the deft politician wanted to completely steer the IR ship towards another direction; this was something that would call for stepping far and beyond the duties (and limits) of a President in this regime. This is also what makes Rafsanjani a pragmatist. He is more pragmatic than he is ideological.
The unexpected nullification of Rafsanjani’s win and call for a re-vote by the Supreme Leadership (SL) in 2005 is justified by some as a defensive move on the Leadership’s behalf. They felt threatened by Rafsanjani. Rafsanjani’s response to SL was instant. His response was a first of its kind in the history of the Islamic Revolution. He publicly questioned not only the SL’s, Khamenei’s, actions re: the election, but he also [dared] question Khamenei’s appointment and legitimacy for the position he holds. This was groundbreaking as far as public discourse of IR officials is concerned.
Rafsanjani repeatedly mentioned that he was in fact more intimate with the deceased Leader Khomeini, than Khamenie was–which is a fact. Relative to Rafsanjani, Khamenei not only lacked in political activism history, he was also not as well read as ayatollah’s usually are. His appointment was made in haste. In the end of the 2005 fiasco, Rafsanjani was appointed a chair position in the Assembly of Experts. This appointment looks more like an attempt to appease, if not set a gag-order, on the rising rebel cleric!
Come back for Part 2 Rafsanjani in the 2009 Presidential Elections

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sorry, what?
The last round of voting was some sort of “run-off” which had not been anticipated. It was in the run-off that Ahmadinejad miraculously jumped up to first place.
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you still have to make it clear that you made a mistake. There was no nullification, no call for re-vote by sl, it was just a second round for none of the candidates could gather 50%+1.