Some time prior to Amaterasu's arrival in Agata Forest, Kokari and his dog Ume found the Tsuta Ruins among the vines and rocks of the cliff surrounding the forest. As they were exploring the ancient site, a monstrous roar echoes throughout the area, scaring Kokari so much that he immediately left the ruins and locked its gate. Only then did he realize that he had left Ume behind, alone to face whatever monstrosities that lurks within the ruins' depths . Unfortunately, Kokari dropped the key to Tsuta Ruins into the Deep Abyss of Agata Forest, and tries to retrieve it with his fishing rod, albeit having no lines.
After Amaterasu restored Agata Forest's Guardian Sapling and encountered Waka for the first time, she found Kokari, standing on the shore of an island in the Deep Abyss, crying. Issun asked him to what was wrong, to which Kokari retold his experience inside the Tsuta Ruins. After briefly motivating the boy so that he could retrieve the key to the ruins (which was swallowed up by a giant salmon) by restoring his fishing line, Amaterasu took the key and went to rescue Kokari's dog by herself, since the boy would put himself in danger .
As Amaterasu entered the ruins, Issun noticed that the water in the area was poisoned, and no living organism could survive in such environment. After traversing the vine-covered ruins, Amaterasu found and destroyed the source of the pollution: five pots pouring a dense, purple poison into the source of the ruins' water, turning the crystal-clear stream into contaminated substance. As the water source was purified, Tsuta Ruins considerably brightened up, and a path into the previously-inaccessible giant Dogu statue in the antechamger was opened. Inside, Amaterasu restored patches of vegetation and re-enabled the automatic sprinkler system created by the ancient civilization that built the Tsuta Ruins, subsequently awakening Tsutagami, who granted her the Celestial Brush technique of Vine. Using this technique, she reached the top of the Dogu statue and entered it, and follows a narrow corridor into the back of the hollowed-out cliff which the ruins is built within, and found a large chamber, where Amaterasu would encounter the first major demon in her journey.
Inside the chamber strung with gigantic spider webs and covered in moss was a huge flower. Closer inspection revealed Kokari's dog Ume sleeping on the pistil in the center of the flower. However, as Issun approached the vegetation, it transformed into the monstrous Spider Queen, which was the entity that awakened upon Orochi's revival . She expressed anger at who would interfere with Orochi's rise to power, and threatened to devour Amaterasu for doing so. Subsequently, the sun goddess and the arachnid demon fought a vicious fight, ending in Spider Queen's destruction. Her abdomen transformed from a hideous plant to a beautiful and pure lotus blossom, and a sense of tranquility flowed throughout the Tsuta Ruins as the demonic forces within the site was eradicated. Ume had survived the ordeal, and was carried back to Kokari.
The ruins still could only be observed from a distance, as the entrance was blocked by earth after Agata Forest's flooding.
- Enhancing Divinity: Near the entrance of the ruins.
- Godhood Tips: To the left of the base of the staircase immediately before battling the Spider Queen.
- #18: After the encounter with Blockhead. On the alcove nearest to the bridge up above in the room (connected to the bridge via a tree trunk ramp), behind the clay statues is a strangely-looking wall that can be destroyed with Cherry Bomb. Inside is a secret chamber with a Giant Bud, using Bloom on it will yield the Stray Bead.
- #19: After clearing the poison from the ruins' water source. Behind the waterfall in the room is another secret chamber with a Stray Bead-holding Giant Bud. Bloom the vegetation to obtain the bead.
- #20: In the hall where the first Bud Ogre is encountered and the crystal sphere is placed, look for a Konohana Blossom above the hall, use Vine to reach it, where another Giant Bud is. The Stray Bead it will release, should it be Bloomed.
- This dungeon shares a name with a Celestial Brush god, Tsutagami.