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In the Star Trek: Voyager  episode "Blink of an Eye", Voyager is stuck in orbit of a planet with a tachyon core which causes time on the planet to elapse at a much faster rate than normal.

Voyager's visible presence has a great effect on the planet's culture and technology, as centuries pass on the surface below. Eventually, the Doctor is sent down to the planet to investigate. He was intended to only spend 48 hours there, but ends up spending three years.

The inhabitants of the planet send up their own astronauts to Voyager, and the Doctor has the following conversation with the one who survives:

EMH: Find out what happened to a boy named Jason Tabreez. He lived in the Central Protectorate.

GOTANA-RETZ: Jason? An unusual name.

EMH: Yes. He was my son.

GOTANA-RETZ: But you're a hologram.

EMH: It's a long story.

This naturally leads to the following question:

How was the EMH able to have a son?

Presumably, Jason's mother is Mareeza (a woman the Doctor describes as his roommate and "companion" on the planet) but how was Jason fathered? What was the long story ?

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    Adoption? Artificial insemination? Consensual infidelity? – Joe L. Aug 1 '15 at 15:15
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    He already said. It's a long story. – Valorum Aug 1 '15 at 15:15
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    thank goodness that the "Similar Questions" updated when it did, i was just about to ask this myself – Memor-X Mar 21 '17 at 23:27
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TV Canon

Within the main TV canon, the boy is never mentioned again, nor are there any obvious references within the episode to what happened or why he has a son other than that...

"...it's a long story."

EU canon

A longer explanation is found within the short story "Eighteen Minutes" written by Terri Osborne and found in the Distant Shores anthology

In short, the Doctor was working at a local hospital as part of his undercover persona. During this time he met and treated a local woman (Mareeza) for a pre-natal condition. After she was released, he continued his relationship with her. He moved in with her and became her roommate.

The father's identity was not explicitly revealed, although it's fairly clear that he was a smooth-talking lothario who done her wrong. The EMH suspects that it's a sleazoid called Leeram who owns a number of local properties:

After a long silence, a wistful smile slowly appeared. “I can see you want to ask. He’s someone I’d prefer not to think about, Aeson.”
“The baby’s father?”
“Yes.”
At that point, I didn’t care how she knew I had wanted to ask about the father. Instead, I asked her if it was really that bad. She nodded, and said, “The child may be the only good to come of it, and he was almost taken from me before I knew he existed.”

Out of gratitude for his saving her child's life (and in recognition of the closeness of their relationship) she asks the EMH to act as the child's father:

She gave me an unquestioning gaze. “Don’t you dare. Aeson, you’ve been far more of a father to this child than anyone could be. I wouldn’t be holding him if it weren’t for you. He may not be your son by biology. But, in every other way, you’re the reason for his existence. You’ve been dedicated to his well-being since before I was able. I would hope that dedication won’t stop now that he’s born.”

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    Excellent --- thanks. I like the rhyme: Aeson and Jason. – Praxis Aug 1 '15 at 16:30
  • He left him quite easily didn't he!? – ThruGog Aug 1 '15 at 16:41
  • @ThruGog - Actually, if you read the story he did briefly consider try to build/locate some way of blocking the transporter. In the end he decided that his loyalty to the crew of the Voyager and the young age of the child (and the fact that he was able to encourage Mareez into a more fulfilling relationship with a local sport star) was enough to quell his pangs of remorse. – Valorum Aug 1 '15 at 16:44
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    @Richard I was thinking that in the episode he seemed happy to be back and that was all, but then we saw literally none of the story on the planet with the Doctor so that's fair. – ThruGog Aug 1 '15 at 18:58
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    I was thinking that he just hugged Kathryn and B'Elanna and acted like he didn't give a crap at randomly being beamed away from his new life and family with no notice. That always bothered me. – Lightness Races in Orbit Aug 2 '15 at 16:17
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In VOY: "Message in a Bottle", The Doctor says:

"I have even had sexual relations"
"Sex, how's that possible? We're not equipped" (EMH 2)
"Let's just say I made an addition to my program"

So The Doctor has made a couple of special modifications, and is presumably "fully functional". It is possible that when the Doctor made his "special modifications" that he went all the way, allowing him to impregnate a local female.

There is the caveat that this would take an insane amount of programming and replicators could be involved, which the EMH and/or B'Elanna might not be able to do.

So there is the possibility that "Jason" is The EMH's actual son

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    The capacity to have sex doesn't even come close to implying the capacity to have (artificially) biological children. All the programming in the world isn't going to create real sperm – Valorum Mar 5 '18 at 1:18
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    But replicators could... – colmde Mar 5 '18 at 11:04

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