The night of the Kyuubi attack Kushina had twin, With Kushina being weak after giving birth and him not being able to stop the strongest bijuu, Minato decides to summon the Shinigami and ask it to seal the Kyuubi into one of his children at the cost of a sacrifice. However, instead of taking Minato's soul, the Shinigami decides to take Naruto's body parts as payment, turning him to a malformed, limbless child without facial features or internal organs.
After the sealing Minato and Kushina decides keep Naruto's birth a secret and to put him into the orphanage under Nonō Yakushi who decides to help and teach him how to be shinobi to protect himself.
Years later after absorbing some of the Kyuubi chakra from his twin by accident, Naruto was able to gain his skin back along with a new abilities.
Naruto discovered that if he absorbed chakra from all the nine Bijuu, he will be able to gain his missing body parts along with some of the bijuu abilities.
Abilities:
Sensor: Mind's Eye of the Kagura.
The Uzumaki clan unique chakra.
Swordsmanship: creating blades from his arms using his uzumaki chakra.
The ability to absorb chakra from other by physical contact.
Healing Factor: after absorbing some of the kyuubi chakra.
Negative Emotions Sensing: after absorbing some of the kyuubi chakra.
If anyone is interested in this idea please send me a message to my PM. And sorry for my bad english language.