Federal authorities filed charges Tuesday against the 28-year-old suspect in the New York and New Jersey bombings over the weekend, according to court documents.

Prosecutors have charged Ahmad Khan Rahami with use of weapons of mass destruction, bombing a place of public use, destruction of property by means of fire or explosive, and use of a destructive device during and in furtherance of a crime of violence.

Investigators said they believe he planted bombs in New York City, as well as Elizabeth and Seaside Park, N.J. One of the devices exploded in Manhattan Saturday night, wounding 31 people.

In addition to the charges, the court filing makes clear that there was significant premeditation that Rahami began online purchases in June and by July was purchasing bomb components, including shrapnel.

Prosecutors allege that two days before bombing in New York City, Rahami did a trial run, lighting an incendiary device.  The document strongly suggests that the bombings were not spur of the moment decision.

Ealier on Tuesday, a law enforcement source close to the investigation told Fox news that moments after the dramatic shootout that ended with the capture of bombing suspect Rahami in New Jersey, police recovered his journal which included references to Usama bin Laden and the American terror cleric Anwar al-Awlaki.

Rahami’s father also claimed he called the FBI on his own son two years ago — but a source said he immediately recanted. And according to a neighbor, the father said in 2014 that his son may have been in contact with people overseas collecting explosives, ABC News reported.

The notebook that turned up on Rahami, pierced with a bullet hole, also included writing that referenced “killing the kuffar,” or unbeliever, a senior law enforcement official told The New York Times.

Rahami’s father, Mohammad, spoke to reporters outside his home in Elizabeth, N.J. “Two years I called the FBI, my son, he’s doing very bad, OK? But they check it almost two months… They say he’s not a terrorist. I said, ‘OK.’ Now they say he is a terrorist. I say, ‘OK.'”

Rahami’s father said that two years ago, his son “was doing bad. Yeah, he stabbed my son, he hit my wife and I put him to jail two years ago.”

Mohammad Rahami added that Ahmad stabbed his brother Nasser “for no reason.” Later Tuesday, he told reporters that FBI agents “[did] not do their job.”

The FBI’s Newark field office looked into the accusations, a federal law enforcement source told FoxNews.com. Ahmad Khan Rahami was in jail on an assault charge at the time, the source said, but agents interviewed his father.

“He recanted immediately – he left that part out. He said he didn’t mean his son was a terrorist, just that he was interested in gang activity and watching violent videos. There was no derogatory information on him, and no basis to continue the investigation,” the source said.

FBI’s scrubbing of the allegations made against Rahami at the time did not turn anything up — or as a law enforcement source close to the investigation described, the lead “washed out.” Fox News is told a full-blown investigation into Rahami was not opened.

Rahami was arrested for stabbing a person in the leg and possession of a firearm in 2014. But a grand jury declined to indict him, despite a warning from the arresting officer that Rahami was likely “a danger to himself or others.”

While the hunt for Rahami has ended, the investigation into his alleged path from server at a family restaurant to terrorist bomber is just beginning. Friends of Rahami’s who spoke with media outlets trace the roots of his radicalism to his trips to jihadist hotbeds in Afghanistan and Pakistan.

“It’s like he was a completely different person,” a friend of Rahami’s, Flee Jones, told the Times. “He got serious and completely closed off.”

Rahami’s first documented trip to Pakistan was in 2005, when he visited Karachi as a 17 year old, The New York Times reported. Rahami stayed in Karachi, known as a jihadi hotbed, for a few months before returning to New Jersey in January 2006. In 2011, Rahami made another lengthy trip, visiting Kandahar, Afghanistan, and Quetta, Pakistan. He again visited Quetta from April 2013 to March 2014. Multiple sources told Fox News that Rahami visited Afghanistan at least three times. Rahami was stopped on one trip for secondary screening, but he satisfied the questions and was cleared, a source told Fox News.

Rahami’s activities in Afghanistan and Pakistan are unknown, and authorities said the excursions didn’t raise any red flags at the time. Officials said at a Monday news conference they didn’t know if Rahami had received any weapons or explosives training. He did have a firearms license, however, The Washington Post reported.

But regardless of what he did during these trips, Rahami’s demeanor changed when he came back to New Jersey. Rahami began wearing traditional Muslim robes after one trip to Afghanistan, two friends, Amarjit Singh and Jonathan Wagner, told the New York Times. He grew a beard and began praying in the back of his family’s chicken restaurant.

Rahami also exhibited anti-Western and anti-military sentiment when he was around his young daughter, a former girlfriend, Maria, told FoxNews.com.

“One time he was watching TV with my daughter and a woman in a [military] uniform came on and he told [her], ‘That’s the bad person,’” she said.

There are family influences on Rahami, too. Rahami’s dad, Mohammad, told Wagner that he fought the Soviet Army in the 1980s as a member of the mujahedeen, the same group that spawned Usama bin Laden and a generation of terrorists. Wagner said the elder Rahami didn’t approve of the current U.S.-led fighting in Afghanistan.

One of Rahami’s brothers, Mohammad K., posted at least one jihadist message on Facebook, The Daily Beast reported. While Rahami had little presence on social media, his brother posted a meme in 2013 showing extremist fighters with the quote: “I bring men who desire death as ardently as you desire life.” The same brother also posted a 9/11 conspiracy theory video last month.

Rahami’s social life also was upended.

He stopped seeing Maria, allegedly ceased paying child support and in 2014 married a woman in Pakistan. He wrote to New Jersey Rep. Albio Sires that year seeking a visa to get his wife into the U.S. Sires said Rahami was “kind of nasty.”

“At the time she was pregnant and in Pakistan,” Sires said on MSNBC. “They told her that she could not come over until she had the baby, because she had to get a visa for the baby.”

The wife, who has not been identified, was eventually allowed into the U.S. She returned to Pakistan just days before the New York and New Jersey bombings and was detained by authorities in the United Arab Emirates on Monday, a U.S. official told The Los Angeles Times.

Separately, a sister of Rahami’s accused him of trying to stab her but later recanted, Rep. Peter T. King, a member of the House Homeland Security Committee, told The Washington Post.

Rahami was born in Afghanistan in 1988 and came legally to the U.S. in January 1995, several years after his father arrived in America as an asylum seeker, CNN reported. Rahami became a naturalized citizen and was known as a “class clown” in high school, Maria told FoxNews.com. Maria said Rahami got along with his classmates; however, he still criticized American culture, comparing Western values to the strict version of Islam practiced in Afghanistan.

Rahami majored in criminal justice at Middlesex County College in Edison, N.J., but he dropped out of school before finishing his degree, according to media reports.

Mohammad reportedly opened First America Fried Chicken in 2002 on the ground floor of a home in Elizabeth. Family members lived on the second floor. It’s unclear when Rahami last lived at the address, but the location was raided by authorities on Monday during their dragnet for Rahami.

Zobyedh Rahami, who said she was a sister of Ahmad’s, wrote online, “I would like people to respect my family’s privacy and let us have our peace after this tragic time. I would not like to answer any questions.”

FoxNews.com’s Perry Chiaramonte, Fox News’ Matt Dean, Kathleen Foster, Catherine Herridge and The Associated Press contributed to this report.