A hand-scrawled confession condemning U.S. actions in Muslim countries was found on the inside wall of the boat where Tsarnaev was captured four frantic days later.
A year after twin pressure cooker bombs shattered the marathon and paralyzed the area for days, federal prosecutors say they have a trove of evidence ready to use against the surviving suspect, but many questions remain.
What roles did Dzhokhar Tsarnaev and his older brother, Tamerlan, play in planning and orchestrating the attack? Would they really have launched a second attack in New York? Did federal authorities underreact to a warning from Russia that Tamerlan Tsarnaev was becoming radicalized?
With Tamerlan Tsarnaev killed in a police shootout days after the attack, some of those questions may never be fully answered.
"The obvious one is the motivation and how could two young men who were in a country that, from all appearances, was very good to them end up this radical," said former Boston Police Commissioner Ed Davis, who helped lead the investigation.
The bombings last April 15 killed three people and injured more than 260 near the finish line of one of the world's most famous marathons. At least 16 people lost limbs.
Dzhokhar has pleaded not guilty to a 30-count federal indictment that carries the possibility of the death penalty.
The brothers, ethnic Chechens who lived in the former Soviet republic of Kyrgyzstan and the Dagestan region of Russia, settled in Cambridge, outside Boston, after moving to the U.S. as children with their family more than a decade ago.
Dzhokhar's defense team, which includes two of the nation's top anti-death penalty lawyers, appear to be building a case that Tamerlan, 26, was the driving force behind the bombings. In court documents, they've focused on Dzhokhar's young age - 19 at the time of the bombings - and the influence his older brother had on him.
A congressional report released last month said U.S. intelligence agencies missed a chance to detain Tamerlan when he returned from a trip to Dagestan in July 2012.
Russian authorities had warned the FBI in 2011 about Tsarnaev becoming radicalized. The FBI investigated, and his name was added to a terrorism watch list. But he was still able to fly to Dagestan - an area that has become the center of an Islamic insurgency - spend six months there, and return to the United States.
"There was not sufficient weight put on the information we got from Russia," said U.S. Rep. William Keating, D-Mass., a member of the House Committee on Homeland Security.
A separate report found that Russia was unresponsive when pressed by the FBI for more details.
Three days after the bombings, the FBI released photos of the Tsarnaevs from surveillance video near the bombing sites. Hours later, authorities say, the brothers shot and killed a Massachusetts Institute of Technology police officer in an attempt to steal his gun, then carjacked a Cambridge man.
"'Where's your money?'" carjacking victim Danny Meng said Tamerlan Tsarnaev demanded of him after jumping into his car and showing him a gun.
What Meng thought would be a quick robbery became more terrifying when the man asked him whether he knew about the marathon bombings.
"He said, 'Do you know who did that? I did that.'"
Meng said Tamerlan asked him, "Can your car drive out of state, like to New York?"
A week later, former New York Police Commissioner Raymond Kelly said Dzhokhar Tsarnaev told investigators from his hospital bed that he and his brother decided that night to drive to New York City and launch a second attack.Meng escaped by running when the Tsarnaevs stopped at a gas station. Authorities said the brothers drove to nearby Watertown, where a wild gun battle with police erupted on a quiet side street, with the brothers shooting at officers and throwing three pipe bombs and one pressure cooker bomb.
Tamerlan Tsarnaev was killed, but Dzhokhar escaped on foot, leading to an unprecedented lockdown of Greater Boston. Dzhokhar, wounded from gunfire, was found later that day hiding in a dry-docked boat in a backyard.
Authorities said Dzhokhar wrote in pen on the inside wall of the boat explaining that the bombing was meant to punish America for its actions overseas.
"The U.S. Government is killing our innocent civilians," authorities say he wrote, and "Stop killing our innocent people and we will stop."
A federal grand jury continued to investigate months after Dzhokhar was arrested.
The parents and sisters of Tamerlan Tsarnaev's widow, Katherine Russell, were called to testify. Russell has a 3-year-old daughter with Tsarnaev.
Russell's lawyer, Amato DeLuca, said that she did not suspect her husband of anything and that nothing seemed amiss after the bombing. He said Russell was told last year she was not a target of the investigation.
"It really saddens me to think the people, obviously innocent victims, are going to carry the wounds from this craziness the rest of their life," DeLuca said. "That includes Katie and her daughter."
People who knew Dzhokhar say they still struggle to reconcile the seemingly Americanized young man they knew with the one accused of planting the bomb that killed Martin Richard, 8, and Lu Lingzi, 23, a Boston University graduate student from China. The first bomb, allegedly planted by Tamerlan, killed Krystle Campbell, 29.
Luis Vasquez, who helped coach Dzhokhar's soccer team in high school, said both brothers appeared to be good people when he knew them. The death penalty, he said, would be the easy way out.
"That event should eat at him," Vasquez said. "If we kill him, he will take those answers with him."
Associated Press writers Paige Sutherland in Boston and Michelle R. Smith in Providence, R.I., contributed to this report.