The legend is that when Valmiki prayed to Lord Ranganatha and Goddess Ranganayaki in the base temple, they took the form of Lord Rama and Sita. The Sesha, Conch, Chakra appeared as Lakshmana, Bharata and Shatruguna and Garuda as Hanuman. Sage Valmiki could view Lord Ranganatha, Lord Trivikrama and Lord Narasimha in the top temple.
This Thiruneermalai Kshetram is also called as "Thoyagiri Kshetram" and also as "Thothadri". Thoya means "Water" and Adhiri means "Mountain" (malai). Since the mountain is surrounded by water, this sthalam is named as "Thiru Neermalai".The Perumal shows his 4 sevas in this temple (ie) - Nindra, Iruntha, Kidantha and Nadantha Thirukkolmas.
It is said that once Thirumangai Alwar came here to get the Dharshan of the Perumal. At that time, the mountain was fully surrounded by water and he waited for six months to worship the Perumal. After all the water drained, he went up the mountain and worshipped the Perumal. The place where Thirumangai Alwar stayed is called as "Thiru Mangai Alwarpuram".
Moolavar :The Perumal gives his seva in four different positions.Sri Neervannar - Nindra Thirukkolam.Lord Narasimhar - Irundha Thirukkolam.Lord Ranganathar - Kidantha Thirukkolam.and Lord Thiruvikraman - Nadantha Thirukkolam. The Neervannar is found in Nindra (standing) thirukkolam facing his Thirumugham towards East direction.
He is also named as Neelamugil Vannan. Prathyaksham (seva) for Thondaimaan, Brighu Munivar and Maarkandeyar.Lord Ranganathar is found in Kidantha (lying) position facing his thirumugham towards South direction and the Sayana kolam is referred to as "Manicka Sayanam". He is lying on the Aadhiseshan under Ranga Vimaanam.
Thaayar:The Thayaar of this sthalam is Sri Animaa Malar Mangai and found in a separate Sannadhi.According to Thirumangai Alwar, Thiruneer Malai is referred to:Thirunaraiyoor - Nindra Thirukkolam,Thiruvaali - Narasiman (Irundha Thirukkolam),Thirukudanthai - Aarai Amuthai (Kidantha Thirukkolam) and Thirukoviloor - Ulagalanthaan (ThiruVikrama kolam).
Thus, in Thiruneermalai Divyadesam, we can see all the four forms of the Perumal together.In this temple, Valmiki Maharshi has worshipped Eari Kidantha (Aranganathan), Iruntha (Narasimar), Nadantha (Thiruvikraman) Kola seva of the Perumal. After worshipping all the 3 sevas, he came down from the mountain to worship Lord Rama. Knowing this Lord Vishnu gave darshan as Sri Ramar and Lakshmi Piratti as Seetha and Aadisesha as Lakshman and Sangu and Chakram as Baratha chatrukanan. Lord Vigneshwar as Sugreev and Garudan as Hanuman.