A CBI team on Friday arrested Swami Aseemanand, the most high-profile accused in the Ajmer Sharif and Mecca Masjid blasts of 2007, in Haridwar on Friday.
They also picked up Brahmanand Maharaj, who had given him shelter, for questioning.
Aseemanand is believed to be the ideologue of Hindu right-wing group Abhinav Bharat, which also allegedly masterminded blasts in Malegaon in Nasik, Maharashtra in 2008.
The swami is accused of having played an important role in funding the explosions in Ajmer and Hyderabad.
Police sources said Swami Aseemanand came for the first time to Bahadrabad village near Haridwar on November 14 and took shelter at Brahmanand Maharaj's ashram.
He was under treatment. It has not been established if he is in league with Brahmanand Maharaj.
"On November 18 at 11 pm, the CBI team picked up Swami Brahmanand from the ashram and Aseemanand from his hut (on the premises)," Haridwar special superintendent of police Sanjay Gunjiyal told HT .
Born Jatin Chatterjee, the swami's story seems like a page out of Bankim Chandra Chatterjee's Anandamath, a novel about Hindu revivalism.
He travelled a long way, from a boy in Hooghly in West Bengal to a cult figure in the tribal areas of Dangs, Gujarat.
After completing his master's degree in physics at Burdwan University in Bengal, he joined the Vanvasi Kalyan Ashram, an organisation inspired by the Rashtriya Swayamsevak Sangh, in 1978.
In Gujarat, he was involved in reconverting tribals from Christianity to Hinduism. He also established a temple there.
Investigators said his interrogation held the key to solving the blasts at the Mecca Masjid in Hyderabad on May 18, 2007, at the shrine of Khwaja Moinuddin Chisti in Ajmer on October 11, 2007, in Malegaon and Modasa on September 29, 2008 and on the Samjhauta Express on February 18, 2007.