Lee, 18, disappeared on 13 January 1999 after leaving Woodlawn High School in Baltimore, Maryland.
Her body was found around one month later buried in a shallow grave in Leakin Park in Baltimore. She had been strangled.
Her car was found abandoned weeks later.
Syed, who was 17 at the time and had recently split up from Lee, was arrested and charged with her murder. In 2000, he was convicted of murder, robbery, kidnapping and false imprisonment and sentenced to life in prison.
After spending more than two decades fighting to prove his innocence – and with his case gaining international attention through the Serial podcast – Syed’s sentence was overturned on Monday and he has finally returned home to his family.
But, with Syed’s conviction now quashed, what happens next?
Will Syed be retried for Lee’s murder?
Will one of the other suspects face charges?
Or is the case now cold?
Firstly, Syed isn’t entirely free just yet.
On Monday, Baltimore City Circuit Judge Melissa Phinn ordered the 41-year-old to be released on his own recognizance and placed on home detention with GPS monitoring.
Under state law, the prosecution now has 30 days to decide whether to drop the charges against him or to set a date to give him a new trial.
Outside the courthouse on Monday, Baltimore City State’s Attorney Marilyn Mosby stopped short of saying Syed is innocent of Lee’s murder and did not exonerate him.
Instead, Ms Mosby said that Syed – whether innocent or guilty – should have been given a fair trial.
Last week, Ms Mosby had filed a motion calling for his release, listing several issues with Syed’s 2000 conviction.
This includes evidence about two other potential suspects which was not handed over to the defence, the admissibility of cellphone data used to place him at the crime scene and the unreliability of the state’s star witness.
Ms Mosby said that the state is now waiting for the results of DNA testing which it hopes could advance the investigation.
In March, prosecutors and Syed’s defence attorneys filed a joint request for Lee’s clothing to be tested using new touch DNA testing, which was not available at the time of the original trial. The analysis came back in August without anything conclusive.
But, Ms Mosby said on Monday that further testing is currently under way and that this will be fast-tracked to try to uncover new information ahead of the 30-day deadline.
She added that if the tests come back with Syed’s DNA, then her office would pursue a new case against him.
However, legal experts say that the chances Syed will face a retrial is “extremely unlikely”.
Duncan Levin, former assistant district attorney in the Manhattan DA’s office and a prominent criminal defence attorney at Levin & Associates who has represented clients including Harvey Weinstein and Anna Sorokin, told The Independent on Tuesday that he thinks this marks the end of Syed’s two-decade long legal battle.
“This is pretty much the end of the road,” he said.
“This was the prosecution’s motion to vacate the sentence so I think they’d like some time to probably tidy up the file but at this time I think it’s extremely unlikely that he’ll get a new court date in the next 30 days.”
However, that doesn’t necessarily mean that prosecutors believe he is innocent, explained Mr Levin.
“Whether he is guilty or innocent the right thing to do at this point is to drop the charges against him,” he said.
“There’s enough doubt about his conviction that it’s clearly the right thing to do.
“This has been a long road and anyone who has been following case – which is millions of people – has reached the conclusion that there is enough doubt about his conviction to vacate it and for the charges to be dropped.”
He added: “There’s a distinction: they’re not declaring him innocent but there’s enough doubt that it cannot stand.”
Mr Levin said that it is unlikely that prosecutors don’t know already what they will do when the 30-day deadline comes around.
“I can’t imagine that they don’t know what direction they’re going in,” he said, adding that he thinks it’s likely that they are already planning to drop all charges against the 41-year-old.
If Syed’s charges are dropped, then Lee’s murder becomes unsolved.
According to Ms Mosby’s office, the two alternate suspects are credible and were both known to the initial murder investigation.
One of the suspects had a motive to kill Lee and had threatened to “make her disappear, to kill her,” prosecutors said.
The two suspects have not been named but investigators are said to be keen to speak to them as they seek to bring justice to Lee’s family.
“For the family members of the 18-year-old girl who was murdered, [the prosecutors] have an obligation to find out [who is responsible],” said Mr Levin.
It is of course possible for prosecutors to bring fresh charges against Syed sometime in the future, if new evidence comes to light once the 30 days passes and the current charges are dropped.
But, given the “holes” in the case against him, Mr Levin said this is also “highly unlikely”.
“I think it’s highly unlikely that prosecutors will recharge him,” he said.
“This is probably the end of the line for the case. They’ll keep looking into it, but it’s a pretty stale case at this point.
“For Mr Syed at least I think it’s the end of the line.”