Predictably, this was reported to the king who was impatiently waiting for the horses to arrive. Manikkavachakar was imprisoned and tortured. Shiva, however, came to his rescue. The miraculous interventions of the deity on more than one occasion deeply moved the King. He begged forgiveness of Manikkavachakar and tried to persuade him to resume his post as minister. The saint refused, and embraced the life of a wandering ascetic. He had an eventful life, composed a sizeable number of hymns in praise of Shiva and, eventually, he settled in Chidambaram where, it is said, he merged into the god.

In the course of the centuries, the temple has been restructured. The inscriptions engraved on its walls do not pre-date the period of the Arantangi Tondaimans who ruled in this area from the 15^th to the 18^th centuries. The large detached mandapa opposite the entrance gopura dates probably of the late 17^th or early 18^th century, and the paintings decorating its ceiling date of the 19^th centuries. Particularly noteworthy is the 18^th century set illustrating the 275 Shaiva holy sites, probably the only one surviving. It is laid out on the ceiling of the pillared hall in front of the Nandishvara Manikkavachakar shrine. The murals on the walls of the corridor around the above mentioned shrine, although in a parlous condition, may date of the late 17^th or early 18^th century. Their present dilapidated state makes it very difficult to establish an approximate date.  A further set of paintings, probably of the same period, is adorns the ceiling of the Panchatchara mandapa, in the outermost enclosure of the temple.

The murals on the walls of the Sivananda Manikkavachakar shrine illustrate in great detail the life of Manikkavachakar. Those on the walls of the prakara surrounding it depict the most important aspects of Shiva as well as the lives of the Shaiva saints as related in the Periya Puranam. Both series date probably of the late 19^th or early 20^th century and are particularly interesting as they clearly reveal the growing influence of Western painting.