Background
Ayatollah Khomeini was a senior Islamic jurist cleric of Shia (Twelvers) Islam. Shia theology holds that Caliphate or Islamic leadership belongs to divinely-appointed line of Shia Imams descended from the Prophet Muhammad, the last of which is the 12th Imam, Muhammad al-Mahdi. The God-given (Infallible) knowledge and sense of justice of the Imams makes them the definitive reference for (Shia) Muslims in every aspect of life, religious or otherwise, including governance. However, the twelfth Imam disappeared into what Shia believe is "occultation" (ghaybat) in 939 AD and so has not been present to rule over the Muslim community for over thousand years.
In the absence of the Imam, Shia scholars/religious leaders accepted the idea of non-religious leaders (typically a sultan, king, or shah) managing political affairs, defending Shia Muslims and their territory, but no consensus emerged among the scholars as to how Muslims should relate to those leaders. Shia jurists have tended to stick to one of three approaches to the state: cooperating with it, becoming active in politics to influence its policies, or most commonly, remaining aloof from it.
For some years, Khomeini opted for the second of these three, believing Islam should encompass all aspects of life, especially the state, and disapproving of Iran's weak Qajar dynasty, the western concepts and language borrowed in the 1906 constitution, and especially the authoritarian secularism and modernization of the Pahlavi Shahs. Precedents for this approach included the theory of "co-working with the just sultan" put forward by Sayyed Murtaza during the Buyid era in his work "Al-Resala Al-Amal Ma'a Sultan" about 1000 years ago, and his idea was developed further by Nasir al-Din al-Tusi. Clerical political influence was institutionalized during the Safavid Empire about 500 years ago. In modern times the Grand Ayatollah Mirza Shirazi intervened against Nasir al-Din Shah when that Qajar Shah gave a 50-year monopoly over the distribution and exportation of tobacco to a foreign non-Muslim. Shirazi issued the famous fatwa against the usage of tobacco as part of the Tobacco Protest.
In 1970 Khomeini broke from this tradition developing a fourth approach to the state, a revolutionary change in Shia Islam proclaiming that monarchy was inherently unjust, and religious legal scholars should not just become involved in politics but rule. (see below)
Read more about this topic: Political Thought And Legacy Of Ruhollah Khomeini
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