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He took him from the world of Atlantis to a parallel world, it is understood, to protect him.

His father then went missing, after submerging into the ocean in his submarine. Before he disappeared he left Jason a pendant - the symbol is the mark of the Oracle, of the Temple of Poseidon - telling him that one day he will understand why. Aided by his Uncle Maguire, Jason goes looking for the wreckage of his father's submarine and finds remains on the ocean floor with the words "The Oracle" printed on it. A bright light appears in front of Jason' sub which pulls him through and he wakes up on the beaches of Atlantis. (The Earth Bull)

Jason's father remains a mysterious character throughout much of the first season, until Jason' parentage is finally revealed in the final episode of Season 1.

In the episode Touched by the Gods - Part 2 the Oracle advises Jason to take Ariadne to the old Silver Mines of Pangeon, in the Mountains of Galena, where she believed they should be safe from Pasiphae and her guards, for she believed they should "not think to look for you amongst the dead". Melas questions the Oracle on the wisdom of her sending Jason to the old silver mines, where she replies "he will be safe there. Who better to protect him than his own father?".    

Aeson and pasiphae

Aeson and Pasiphae

Jason and company escape from Atlantis with Ariadne, after rescuing her from her intended public execution and make their way to these mines. Here, in the caves, they meet a large group of people who have made the caves their home after they had been scorned from society for their disease - "...the living dead. Lepers", as Pythagoras aptly puts it. The apparent leader of the community of lepers addresses Jason and company, inviting them to safely stay in the caves. With recognition he notices Jason's pendant (the one Jason's father left him) and asks Jason of his name. 

When Pasiphae and Heptarian's guards find Jason and companies tracks leading to the caves the leper leads them out the back of the caves. As the guards catch up with Jason and his friends Jason is knocked out in a fight with one of the guards. Pasiphae desires to deal with him herself, sending the guards away. As she goes to slit Jason's throat he leper calls out for her not to harm Jason. "You do not recognise me, yet it was you who made me like this", he announces to her and as she recognises him she mentions him by name, "Aeson". 

It is revealed here that Jason is their son. Pasiphae had believed her son dead, but Aeson tells her that when she had betrayed him and usurped the throne with Minos he took Jason away "somewhere safe, where you would never find him".

So, in the final episode of Season 1 it is revealed, unbeknownst to Jason, that his father is Aeson, the cursed leper and (seemingly) former King of Atlantis and his mother, Pasiphae. The extent of Aeson and Pasiphae' relationship, the details of her betrayal and the subsequent events leading to Jason being sent away is still, as of yet, unclear.  

The oracle wreckage