I honestly believe his mother and king Gerrod are siblings. Even though Rain is older than Kitana, he is not in the immediate line of succession. He and Kitana did not know they were related til after their engagement (referred to the 90s cartoon) to which they broke off the engagement. It is my theory they found out via Raiden or Fujin and this marriage was controlled and contracted by Sindel to keep both in line via marriage.
In the game (MK11), Kitana, Raiden, Fujin, Kotal, and Sheeva in no uncertain terms do acknowledge he is a prince (but not a fit ruler) except Sindel, Shao Kahn, and Mileena.
Why? Why do the only ones who fully deny him being of royal blood are the ones who basically forcibly colonized Edinia?
I also theorize the ones who keep him safe is infact his half brother's and their mother, knowing he is not to blame for being born (nor his mother for being seduced.)
It is also a theory that Sindel is the reason his mother is murdered. She told Argus lies because Rain's mother was planning to warn her brother the king about Sindel's affair with with Shao Kahn (who is also a victim of Sindel's hunger for power).
Please tell me what you think about this, my head hurts from making my caffeine fueled mind actually form sentences.