A pregnant Blair Cramer flew down to Mexico in the fall of 2001 to have her baby, convinced that ex-husband Todd Manning would take the baby away from her if he learned it was his child and not Max Holden's, as Blair claimed. Todd followed Blair to Mexico and delivered a healthy baby boy. But believing the baby to be Max's, Todd told Blair the baby had died and then gave the baby to a pair of Spanish nuns at the airport. When opportunist David Vickers saw the exchange, he convinced the nuns to give him the baby and then forced Todd to pay him a large sum of cash to dispose of the child. David sold the baby to a rich couple in Texas. When Blair later admitted that the child had actually been Todd's, Todd tracked down the baby and brought him back to Llanview, convincing Blair that they should adopt the child. They named the baby John Cramer Manning.

After baby Jack developed aplastic anemia, just like Starr had, Blair learned that Jack was her biological son and ripped into Todd for lying to her. Blair then snuck off to Hawaii with Jack and Starr to get away from Todd. But Todd tracked her down and plotted to kidnap his kids with the help of a man named Ross Rayburn. Blair was tipped off to Todd's plans by his ex-wife, Téa Delgado, and Blair safely returned to Llanview with Jack and Starr.

In 2004, Jack was kidnapped by Margaret Cochran, an accountant at Buchanan Enterprises who was obsessed with Todd. Jack was returned safely after the police caught Margaret. In May 2005, Jack was rushed to the hospital after he lost consciousness and was unable to breath. New doctor Spencer Truman performed an emergency tracheotomy to open his airways, saving his life. When Blair later began dating Spencer, Jack got close to the doctor before everyone realized he was really a psychotic murderer.

As Jack entered preadolescence, he began to exhibit more of his father's mischievous ways. When Blair began dating John McBain, one of Todd's least favorite people, Jack made his animosity known by repeatedly referring to John as "Detective McPain." When Todd prepared to marry Téa Delgado in 2009, Jack blackmailed his father into agreeing to buy him a new car when he was old enough in exchange for serving as best man. He also enjoyed ruffling the feathers of his mother's aunt, Dorian Lord. One time, Jack snapped a photo of Dorian in a compromising embrace with Charlie Banks, which Todd promptly sent to Viki. When Blair got engaged to attorney Elijah Clarke, Jack rightly warned his mother that Eli was up to no good, and Eli eventually was revealed to be a serial killer.

In February 2011, 15-year-old Jack and his band of high school cohorts began tormenting Shane Morasco. They picked on him because of his asthma, nicknaming him "Wheezy," and because his love of comics and lack of money set him apart from the other kids. Shane was afraid to say anything to the adults, and Jack's parents had no idea that their precocious little son had grown into a bully. When Jack and one of his buddies, Brad, stole the booster club money that Shane had been collecting, the boys' parents were called to the school and the money was found in Shane's locker, even though he insisted that Jack had stolen it. Jack vowed to get even on Shane for ratting him out, even though Shane was the one who got suspended.

While in the gym one day, Jack and his buddies started pushing Shane around, causing him to drop his inhaler. Jack took the inhaler and ran out of the gym, leaving Shane behind. Later, he heard that Shane had an asthma attack and would have died if Dani and Destiny hadn't gotten him help. Dani accused Jack of stealing the inhaler, but Jack denied any involvement. Jack and his buddies launched another plan to embarrass Shane by stealing his clothes after gym class, forcing him to come into the gym wearing only a towel. As students recorded Shane on their cell phone cameras, Jack pulled off Shane's towel, leaving him naked and embarrassed. Shane bolted from the gym, just as Starr entered and demanded to know what was going on. Rex and Gigi then showed up and accused Jack of having been bullying Shane for months. With the proof all over MyFace, Jack was unable to deny it. Jack was unrepentant when Blair approached him about the bullying, even saying that Shane had asked for it just like Marty asked to be raped by Todd. Blair slapped Jack and told him he needed to get his act together or he would end up just like his father.

Blair forced Jack to go apologize to Rex and Shane, but an angry Rex told them that Shane had tried to kill himself. When Jack blamed Shane for being weak, Rex got physical with him until Blair intervened. Jack was at Capricorn doing chores as punishment when a couple of thugs came in and began beating Jack up. Tomas pulled off the thugs, and Blair took Jack to the hospital to get his injuries treated. After Todd awoke from his coma, Blair told him what Jack had done and Todd chewed him out.

Jack still didn't seem to understand that he had done anything wrong and continued to plot new ways to torture Shane. Jack couldn't resist poking fun at Shane when he learned Shane was lifting weights at the gym. But Shane got the upper hand when he dropped a weight on Jack's foot. To get even, Jack created a fictional person on MyFace named ComicGirl15 using his friend Brad's computer and friended Shane. Posing as the fictional girl, Jack attempted to lure Shane to a vacant house where he and his friends planned to lock Shane in a basement room. Unbeknownst to them, Shane had figured out what was going on and had told his mother, Gigi, who went instead to the house. The kids didn't realize that it wasn't Shane and locked Gigi in the room. Hours later, Jack ran into Shane and was surprised to see him. Rex put the pieces together and figured out that Gigi was in the vacant house, but once he got there he found her unconscious from carbon monoxide poisoning. John McBain brought Jack in for questioning, but Jack denied having any knowledge of what happened. Brad was brought in after the computer used to create ComicGirl15 was traced back to him. Todd paid off Brad's father's debts in exchange for Brad admitting that he acted alone. Jack was relieved to be off the hook, but Todd made him start working at The Sun so he could keep an eye on him. After Gigi was declared brain dead and taken off life support, Jack began to feel remorse for his actions. He stole Todd's car so he could drive to Shane's house and apologize for what he did, but Todd arrived and cut him off. Rex pretended to accept Jack's apology and make nice with Todd, but he privately told Shane that he would make them pay for Gigi's death.

Jack told Todd that he worried John McBain wouldn't stop until he proved Jack was behind Gigi's attack, but Todd let Jack know that he had a secret weapon to use against John: knowledge that John was the father of Natalie's baby, not Brody. Todd ordered Jack to research a company called Origami Cogs after it bought a company out from under him. Neither realized that the company was set up by Rex, who was out for revenge. Jack was knocked unconscious in Todd's office, and Jack suspected that it was the person behind Origami Cogs. Jack and the rest of the Mannings were stunned when a man resembling Todd before he had plastic surgery showed up in town, claiming to be the real Todd Manning. Todd revealed that he had already met this man and that he was the one who had knocked Jack unconscious, as well as kidnapped Sam. Jack sided with his father, but Starr seemed to believe that the other man was their real father.

DNA tests ultimately proved that both men were identical twins, and their believed-dead mother Irene Manning showed up to explain that she was responsible for trying to pass off Todd's brother, Victor Lord Jr., when Todd went missing 8 years earlier. Jack refused to accept Todd as his father, referring to him as Scarface. In August 2011, Jack was found unconscious outside the hospital and was horrified when John McBain revealed that someone had shot and killed Victor Lord Jr. in his home. Jack was convinced that Todd had killed Victor but Todd swore he was not the killer. Jack took an instant liking to a girl named Neela Patel and agreed to hide her at LaBoulaie when her family wanted to send her back to India for an arranged marriage. Jack set fire to The Sun's offices in retaliation for Todd taking over the paper. When he learned that Neela's brother Vimal and his wife Rama were at the paper, Jack rushed there and freed them. Neela realized that Jack had set the fire but agreed to keep quiet.

After Shane told Neela that Jack had murdered Shane's mother, Jack told Neela about the bullying that had taken place the prior year and said he regretted what he had done. He became more comfortable with Neela and eventually admitted that he was responsible for locking Gigi in the basement. Jack was stunned when the police arrived on Christmas Eve and arrested him for Gigi's murder. Jack learned there was a tape recording of his confession, and Neela admitted that she had set him up. Jack was furious and ordered her out of his life. While Jack was discussing his case with Téa, he was stunned when Shane showed up with a very much alive Gigi. Gigi explained that her sister was the one who actually died after trying to take over her life but said Jack still needed to pay for what he had done. Jack was charged with unlawful imprisonment and freed on bail as he awaited trial. Neela apologized for setting him up and said she believed he was truly sorry for what he had done. Jack said goodbye to his sister Starr, who moved to Hollywood with Hope to pursue a music career.

Jack remained deeply affected by Victor's death and refused to allow Todd to have any place in his life. However, Jack was forced to reconsider his feelings towards his biological father and the father that had raised him after Victor was revealed to be alive. He welcomed the man that he considered to be his father back until Victor left town almost immediately after his return. Meanwhile, Todd remained in Llanview and began spending more time around the house with his mother. Jack feared that his parents would reunite but found a distraction in the bed of an older woman named Kate, who was actually his teacher. Even after Jack and Kate realized that she was his teacher, their affair continued in secret.