Lord Govindaraja is the deity of Chidambaram, one of the 108 Divya desams (Sri Vaishnava kshetras sung by Alwars)
Chidambaram or Thiru Chitrakootam is one of the 108 vaishnava divya desams. The Vaishnavaite sthala purana is supposed to be based on Bhavishyottara Purana??, Kshetra Khanda. Viswakarma is believed to have built Thiru Chitrakootam.
Koyir Puranam? or koyil puranam? a very ancient record speaks of 6th century Pallva King Simhavarman as having worshipped the original deity in Thillai forests.
The stories connected with this divya desam are related to Bhavishyottara puranam, Kshetra khanda in the chapters dealing with Krishna Kshetramahatyam.
The stories connected with this divya desam are told by Vyasa to Jaimini.
In Kritayuga, Sage Kanva performed severe penance on Meru Mountain for number of years.
Lord Vishnu appeared before the sage and asked to choose a boon. Sage Kanva requested for moksha. Lord Vishnu informed him that sage has to live for some more time in this world. Lord Vishnu advised the sage to go to Pundarikapuram where viswakarma had at the behest of Brahma, created a town in the form of lotus. Lord Vishnu asked the sage to go that town at worship him and that in due course of time Lord Vishnu would appear again and grant the sage his wish of Moksha.
Sage Kanva went to the pundarikapuram and in midst of thillai vanam (a kind of mangrove forrest) started doing severe penance. The severity of the penance was so great that Indra and other devas were worried and went to satyaloka to seek Lord Brahma’s advice. Brahma assured them that the penance of sage Kanva was harmless, but still took all of them to Lord Siva. Siva also assured them that the penance was harmless and the sage was praying only for moksha. But inorder to reassure the Indra and devas, Lord Siva took all of them to Ksheera sagara, for Lord Vishnu’s advice. Lord Vishnu assured them and informed the devas that sage Kanva was doing the penance for moksha as adviced by Lord Vishnu.
Lord Vishnu asked all the devathas including to go to Pundarikapuram, as he would soon be appearing in front of sage kanva to grant his wish of moksha.
Soon, Lord Vishnu appeared again before sage kanva. This time the sage wished for four boons.
Lord Vishnu should stay in Thiru Chitrakootam or Chidambaram and give provide succor to all his devotees
Whoever even thought of this place will be blessed with four purusharthas
Those who give up their mortal coils at that place must be granted moksha
Lastly, the he should get moksha.
Lord Vishnu granted all his wishes.
In the meantime, Lord Brahma requested Viswakarma and also maya the divine architects to construct a temple for Lord Vishnu.
Accordingly a beautiful temple was built for Lord Vishnu at Chidambaram.
The vimana was called Satvika vimana. The pancha bhoothas became the five kalasas on the top of sanctum sanctorum. The four vedas became the gopurams and 36 smruti sutras became 36 entrances. The astakshara became the eight steps that lead to sanctum.
On completion of this temple all devas worshipped Lord Vishnu.
Lord Vishnu assumed the sleeping posture (sayana posture) on his favourite couch Adisesha under the satvika vimana and is called Govindaraja. Lord Brahma performed the brahmothsavam for the Lord.
Another Stahla purana is as follws:
Another story related to this divya desam is about Lord Vishnu acting as the Judge watched the dancing contest between Siva and Parvati. One day, Lord Siva was lost in meditation on Lord Vishnu and his divine qualities.
Out of sheer joy, Lord Siva performed Ananda thandava (dance of joy or happiness)
All the devas appreciated the dance. Seeing this Goddess Parvathi got a desire to dance along with Lord Siva.
In course of time, the the dance became a competition between the two viz. Siva and Parvathi.They requested Lord Brahma to give a verdict on who was the better dancer. Brahma expressed his inability and asked them to request Lord Vishnu.
Both, Siva and Parvathi went to Kshira sagara and requested Lord Vishnu to Judge their dance. Lord Vishnu told them that he would witness their dance at Thillai Vanam (a type of mangrove forrest, Chidambaram) and then provide his judgement.
Lord Vishnu reached Chidambaram, went to the Ratna sabha and sat on the throne shaped like Omkara. Siva and parvati started their dance competition. Lord Vishnu laid out the rules prescribed in Bharata sastra and that each should repeat whatever dance mudra performed by the other. In case any one of the them (Siva or Parvati) is not able to perform accordingly, he or she should accept defeat. Also, any violation of bharata sastra will also result in defeat. Whoever is declared as defeated should stay outside the city of Chidambaram. Both Lord Siva and Goddess parvati agreed to the above conditions.
The dance competition started and went for days. As days progressed, parvati was becoming more and more refined and beautiful in dance. Siva felt ashamed that he may be defeated by Parvathi. So, Lord Siva appealed with to Lord Vishnu to help him from the imminent defeat. Lord Vishnu became pleased with Lord Siva’s appeal, took pity on Lord Siva and gave him a hint. Lord Siva quickly grasped the hint (provided by Lord Vishnu) lifted his leg and performed urdhva thandava. Parvati, as a woman, felt ashamed at performing this Urdhva thandava posture. This failure of parvati in performing the dance posture resulted in Siva being declared as winner by Lord Vishnu and Parvathi was to stay outside the city as agreed earlier.
As a result, in the northern part of the town, a small temple was built and Thillai Kaali (Parvathi) is to seen even today.
Lord Siva was so happy that he was declared the winner, informed Lord Vishnu (Govindaraja), that he too would continue to stay at Chidambaram and worship Lord Govindaraja (Lord Vishnu).
Hence it is that Lord Siva known as Nataraja continues to give darshan to devotees in his dancing posture by the side of the shrine of Lord Govindaraja.
At that time, Indra also came to Thiruchitrakootam (Chidambaram) He reminded, Lord Vishnu of his earlier promise to give him a weapon to defeat Valkali, a rakshasa. Lord Vishnu accordingly gave him a weapon and as a thanks offering, Indra celebrated in the month of Vaisakha, a grand festival for 10 days. This story is related in Bhavisyottara purana in the 12th and 13th adhyayas. It is also related in Vyagrapura mahatyam in the 14th adhyaya and chidambara mahatyam in adhyayas(chapters) 25 and 29 - (Reference - 108 Vaishnavaite Divya Desams by M.S.Ramesh, published by TTD publications)
Kulothunga Chola (11-12th century) a fanatic Saivaite king, who was persecuting vaishnavas and forcing everyone to convert to saivism, ordered the removal of Govindaraja's deity from the temple and submerged the deity in the ocean.
When Sri Ramanujacharya visited Tirupati and when he heard the incident of Submergence of Govindaraja deity by Kulothunga Chola, Ramanujacharya decided to create another deity of Govindaraja and consecrated it in the present Govindaraja temple in Tirupati. This temple actually might have been the temple of Parthasarathi (Lord Krishna and Goddess Andal). Ramanujacharya installed Govindaraja deity in that temple. There are separate shrines for Lord Parthasarathi and Goddess Andal.
Infact, TTD has put a signboard containing the same story outside the Govindaraja temple in Tirupati.
The story of Govindaraja being the brother of Lord Srinivasa is more like Lord Oppliappan being called brother of Lord Srinivasa as avatara of Oppliappan was before Lord Srinivasa. Similarly, Govindaraja is considered brother of Lord Srinivasa because his avatara was before Srinivasa.