Naraku did not know how long he had been sealed here. He had thought that, in those final moments, Kagome would purify him along with the Shikon Jewel. But he had been wrong. That had not been the end, but the beginning. Unwilling to vanish, the Shikon Jewel had used every last ounce of its strength at the critical moment to force open the gates of Yomi, intending to rest and recover there for a time.
After all, when Kikyo first died, she had brought it here, hoping to seal it away forever. Unfortunately, the miko's wish had not come true. When she reincarnated, the Shikon Jewel had hidden within her abdomen and seized the chance to escape Yomi, opening a new chapter in the entanglement between the reincarnated miko and the half-demon.
Yet, contrary to the will of the Shikon Jewel's expectations, its final escape had caught the attention of the Hell Lord. Even the Hell Lord could not escape the Demon Jewel's innate ability to draw out the darkness in human nature. Unable to extract his avatar from the jewel, he had no choice but to seal the Shikon Jewel in the deepest reaches of Hell, both to protect it and to keep it under control...
That brief encounter with the Hell Lord had made Naraku realize clearly that he was merely an avatar the other had once wished to discard, just as Onigumo was to him. More ironically still, the Hell Lord could not rid himself of Naraku, and Naraku could not rid himself of Onigumo. Thus, he had taken Onigumo back into his body, while the Shikon Jewel prevented the Hell Lord from touching him with ease.
Naraku did not wish to be absorbed by the Hell Lord, not now that he truly understood his feelings