Finally, with a great effort and making preparations for moving, he left for Qom. In addition to many scientific and spiritual advantages and being under instruction of the senior scholar (allameh) Tabatabaei (1892-1981), this movement was a beginning of his entrance into political activities and a chance to learn about Imam khomeini (1900-1989) and Islamic movement. In his memories, ayatollah Bayat quotes how he met Imam Khomeini and allameh Tabatabaei: "In the early days of my residence in Qom, a religious gathering was held at the house of ayatollah seyyed Ahmad Shobeiri Zandjāni, the father of the grand ayatollah Aqa Moosā Shobeiri.  Since I was a young student, I took part in such gatherings enthusiastically. There I met Imam Khomeini who was called Hajji Aqa Ruhollah and allameh Tabatabaei, so this was the beginning of my acquaintance with them."

He entered the seminary of Qom and there he attended courses to complete advanced ancient textbooks known as saṭh and other lessons such as erth (Islamic inheritance jurisprudence), lomĕ, the collection of laws and treatises of sheikh Ansari, kefayeh, manzume e falsaphe (philosophy in verse), Asfār al-'arba'eh (the four spiritual journeys), makaseb moharrameh, and other lessons. In that period of time, he attended the classes of teachers such as the grand ayatollah Soltani Tabatabaei, allameh Tabatabaei, the martyr ayatollah Dr Muhammad Mofatteh, the martyr ayatollah Morteza Motahhari, ayatollah Muhammad Esmaẻil Sa‛eni, ayatollah Ahmad Pāyāni, the grand ayatollah Montazeri, the grand ayatollah Hossein Noori and ayatollah Mostafa Ẻtemadi and then he attended research courses known as kharij under instructions of Imam Khomeini and at the same time and also during the time when Imam Khomeini went into exile, of senior scholars such as the grand ayatollah Golpaygani, the grand ayatollah Mohaqqeq Dāmād, the grand ayatollah Morteza Ha‛eri, the grand ayatollah Hashem Ảmoli, the grand ayatollah Shariatmadāri, and the grand ayatollah Arāki. Along with studying and teaching, he continued his political activities against the ruling regime and after several times of temporary detention and being forbidden from giving a speech, he, in the year 1972, was arrested by agents of National Intelligence and Security Organization (SAVAK) and was sentenced to one year imprisonment in the prisons of Komite e Moshtarak (standing committee) and Qasr. After being released from prison, he did not abandon his informative and enlightening political activities. He quotes how once was arrested by SAVAK agents: "Those days my house was in Haram Nama alley which past inhabitants know there well. I remember one day after teaching philosophy I returned home and took a nap. I had bad dreams in which a number of scorpions were moving towards me, one of them stuck to my leg, one to my hand and another was almost in my mouth …. I horribly woke and suddenly realised that some unknown men had trespassed on my house. It was weirdly interesting to see how fast my dream had been interpreted and those creatures in my dreams were security agents who had come to arrest me."

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