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Original Timeline Edit
Fauxlivia discovered she was pregnant on a Fringe case. Her fiance Frank Stanton was heartbroken to learn she was six weeks pregnant, which meant that the child could not be his, as he was away on business. Frank leaves Olivia after she admits she loves the father inadvertently. ("Immortality")
His grandmother, Marilyn Dunham, was worried that he had an in-utero disease, Viral Propogated Eclampsia (VPE), that would result in the death of either the baby or his mother during birth. To prevent this occurrence, his mother was abducted by a group of doctors that sped up the pregnancy under Secretary Walter Bishop's orders. She was, after some time, able to escape the place where she was being held and gave birth to him, with the help of Henry Arliss Higgins and Lincoln Lee in a Chinatown store. Because the pregnancy was sped up, the disease was not fully developed, allowing for both Henry and Olivia to survive the birth. Under Secretary Bishop's command, the doctors sampled his DNA and delivered it to Walternate. ("Bloodline")
He was later seen in a baby stroller being taken for a walk in a park by his mother and nanny. When his mother had to go, Mary took over and told Olivia that he would be safe with her. Before she leaves, Olivia said goodbye to Henry - the first time his name was used. Presumably, she named her son Henry in honor of the help Henry Arliss Higgins gave her in delivering him. When Olivia planned to betray Secretary Bishop, she told Lincoln to deliver Henry to his grandmother Marilyn for care if she did not return by the next day. ("6:02 AM EST")
Alternate Timeline Edit
In the alternate timeline, Henry's father, Peter Bishop, was erased ("The Day We Died"). September made a different choice during this time, and decided not to save Peter, and thus he drowned as a child at Raiden Lake. ("Neither Here Nor There") Therefore, Olivia never met Peter, and never gave birth to Henry. Her relationship with Frank remained intact for a while longer. ("One Night in October")
When a returned Peter went inside September's mind, the Observer informed Peter of Henry's prior existence and explained that Peter was erased from existence because Henry was never supposed to be born. Instead, Peter was supposed to have children with Olivia Dunham from the prime universe; Henry's existence was an event that changed the timeline too much for the Observers to compensate for, so they opted to erase Peter to solve the problem. ("The End of All Things")