If there was one theme among many of the city’s top stories for 2019, it was that the news wasn’t quite what it seemed.

“Empire” actor Jussie Smollett made global headlines when he said he’d been the victim of a racist, homophobic attack downtown. Then other details trickled out that suggested a far more complicated story.

Chicago Supt. Eddie Johnson’s 31-year career — 3 1⁄ 2 as the city’s top cop — looked set to end with a pat on the back and a chorus of praise for his many years of service. But a month after he announced plans to retire, a fuming Mayor Lori Lightfoot canned him — saying he’d lied to her about an incident in October when he was found asleep at the wheel of his car.

The beginning of the year brought federal attempted extortion charges against Ald. Ed Burke, but by year’s end, it became clear the feds had cast a far wider net in an on-going public corruption probe. Here, in no particular order, are our picks for the top local stories of 2019:

LORI LIGHTFOOT

In a field of 14 that included Cook County Board President Toni Preckwinkle and former U.S. Secretary of Commerce Bill Daley, Lori Lightfoot’s campaign for mayor looked destined to become a mildly interesting footnote in city politics.

But not only did the former federal prosecutor make it out of the first round, she clobbered Preckwinkle — an early frontrunner — in the April runoff after an at-times bitter race. The city had embraced the outsider, as well as its first openly gay African American woman mayor.

Speaking before thousands at her May 20 swearing in, Lightfoot thanked her 90-year-old mother, who sat proudly in the front row at Wintrust Arena. And Lightfoot promised to be a different kind of mayor.

“I campaigned on change. You voted for change. And I plan to deliver change to our government,” the new mayor said.

After returning to City Hall, Lightfoot made good on a key campaign pledge by signing an executive order stripping aldermen of their absolute power over licenses and permits in their wards.

JUSSIE SMOLLETT

Even if you’ve never seen the show “Empire,” chances are you now know more about one of its former stars, Jussie Smollett, than you could possibly have imagined at the start of the year.

The Smollett saga, which has had more twists and turns than San Francisco’s famously crooked Lombard Street, began in January when the openly gay actor told Chicago police he’d been the victim of a racist and homophobic attack downtown that involved two men beating him and putting a noose around his neck.

But something about Smollett’s account didn’t seem quite right to a lot of folks, including the claim his attackers yelled the actor was in “MAGA country.”

A very different story emerged after police tracked down and interviewed Smollett’s two alleged attackers, who said the actor paid them to help stage the assault. Sixteen felony disorderly conduct charges followed for Smollett. The plot thickened when those charges were suddenly, and without explanation, dropped – with suggestions that Cook County State’s Attorney Kim Foxx’s office had given the actor special treatment, something Foxx strongly denied.

Smollett continued to say he was the misunderstood victim. And the story continues, with a special prosecutor investigating the decision to drop the charges and the city suing to recoup the $130,000 it says it cost for the police investigation.

CHICAGO TEACHERS STRIKE

The new mayor’s goal was to avoid the sea of Chicago Teachers Union red that swarmed around City Hall shortly after her predecessor took office. Lightfoot would offer teachers of the nation’s third-largest school district a 16% raise over five years in the hopes of averting a strike.

Some said she showed her hand too soon. Others said the rookie mayor miscalculated how tenacious the union would be about the rest of its demands.

So in mid-October, teachers took to the streets, leading to a walkout that would last 11 school days – the longest teachers strike in three decades. Frustrated parents scrambled to find care for their kids, while teachers accused Lightfoot of betraying her pre-election promises to them.

“We are enormously disappointed that CTU cannot simply take yes for an answer,” Lightfoot told reporters at City Hall the night of Oct. 27.

Students finally went back to school after the mayor agreed to make up five of the missed school days, funding some of the teachers’ lost pay.

EDDIE JOHNSON

The city’s top cop announced in early November he was stepping down after 31 years with the department — 3½ as superintendent.

“It’s time for someone else to pin these four stars to their shoulders,” a misty-eyed Supt. Eddie Johnson said.

Neither Mayor Lori Lightfoot nor Johnson mentioned a mid-October incident, when the superintendent was found asleep in his car near his Bridgeport home. At the time, he said he neglected to take a prescribed medication and became lightheaded before he decided to pull over, but Lightfoot said he told her that he also had a couple of drinks before driving home.

Then Lightfoot got a look at Inspector General Joe Ferguson’s report about the incident. On Dec. 2, a fuming Lightfoot said she had canned Johnson, saying he had “intentionally misled the people of Chicago and he intentionally misled me. None of that is acceptable.”

The mayor wouldn’t share specifics, but sources told the Chicago Sun-Times that Johnson had spent three hours on Oct. 17 drinking at a restaurant near the Chicago Board of Trade with a woman he had promoted to his security detail shortly before becoming the city’s top cop.

In a prepared statement, Johnson denied intentionally misleading anyone. At year’s end, multiple Chicago police employees were under investigation for allegedly engaging in a widespread cover-up to protect Johnson and conceal the circumstances surrounding the drinking incident.

R. KELLY

A Cook County jury acquitted R. Kelly of child porn charges in 2008, but the rumors about the R&B star’s off-stage behavior never went away.

Then came the Lifetime documentary “Surviving R. Kelly,” which aired in early January, spotlighting new and old allegations against the performer. Soon after, Cook County State’s Attorney Kim Foxx said her office had been inundated with calls about the allegations in the documentary.

Then in February, Foxx’s office charged R. Kelly with 10 counts of aggravated sexual abuse. Federal charges in Illinois and New York followed. Kelly has pleaded not guilty to all of the charges against him.

In an interview with CBS News’ Gayle King, Kelly declared: “I’m not a devil, and by no means am I a monster.”

At one point, Kelly, his voice choked with emotion says, “I didn’t do this stuff. This is not me! I’m fighting for my [expletive] life!”

By year’s end, Kelly remained locked up in a downtown federal cell, awaiting trial in April on child porn and obstruction of justice charges.

BABY CUT FROM WOMB

Clarisa Figueroa’s deception began in late 2018, when the middle-aged South Side woman began telling family members she was pregnant.

She even posted pictures of ultrasounds online, even though she wasn’t actually expecting a baby. The charade reached its horrific conclusion in April, Cook County prosecutors say, when — with the help of a 24-year-old daughter — she lured a pregnant woman to her Scottsdale neighborhood home, strangled her and cut her baby from the womb. At the time, Marlen Ochoa-Lopez was responding to a Facebook ad for free baby clothes, prosecutors said.

Figueroa and daughter, Desiree Figueroa, allegedly dumped Ochoa-Lopez’s body in a garbage can and then called 911. Clarisa Figueroa claimed she’d just given birth and her baby was not breathing. DNA testing proved the baby didn’t belong to Figueroa. Murder charges for Figueroa and her 25-year-old daughter followed in a story that made international headlines.

The baby died in June. Clarisa’s boyfriend, Piotr Bobak, has also been charged in the case — accused of concealing a homicide. All three have pleaded not guilty.

HUMBOLDT PARK ALLIGATOR

As far as alligators go, this one was a little on the puny side — about 4½ feet long, a hair over 30 pounds.

And it wasn’t the first gator to get loose in the city. Perhaps it was its ability to outfox Chicago’s own “Alligator Bob.” Or the fact a shaggy-bearded wrangler from Florida had to be summoned to get the job done.

Whatever the reason, Chicagoans — and much of the rest of the nation — were, for a few days in July, captivated by the hunt for the Humboldt Park lagoon reptile.

“It’s one of those things [that] if you have enough want to, you accomplish whatever you want to,” said Frank Robb, the Florida man who captured the gator using a fishing rod and a secret vocal technique he learned from his uncle, “Gator Bill.”

Robb became an instant hero. He was invited to throw out the opening pitch at a Cubs game. And his cool-under-fire technique made him a catch for one Chicago woman.

“This might be love,” Robb told the Sun-Times in August.

ONGOING FEDERAL PROBE

Federal prosecutors rang in 2019 by slapping Chicago’s longest-serving alderman, Edward M. Burke, with attempted extortion charges Jan. 2. In the weeks that followed, the Chicago Sun-Times revealed then-Ald. Danny Solis had worked with the government to record Burke, and the newspaper exposed the contents of a bombshell affidavit. The document not only contained salacious details about an investigation of Solis, it revealed the FBI had secretly recorded House Speaker Michael Madigan.

That was a fitting start to a year that would also see the feds charge state Sen. Thomas Cullerton with embezzlement and state Rep. Luis Arroyo with bribery, prompting him to leave office. The feds also revealed the cooperation of another elected official — a state senator — who they say secretly recorded Arroyo. A source told the Sun-Times that person is Sen. Terry Link, though Link has denied it.

Burke would also eventually be hit with a 59-page racketeering indictment.

Additionally, halfway through the year, federal prosecutors secured the cooperation of another key player, longtime Chicago Teamsters boss John T. Coli. The labor leader agreed to “fully and truthfully cooperate in any matter in which he is called upon to cooperate” when he pleaded guilty in an extortion case in July.

While other politicians may not have been charged, many appear to be in the crosshairs of multiple, ongoing criminal investigations into public corruption. Raids by the FBI in 2019 targeted Ald. Carrie Austin, state Sen. Martin Sandoval, Cook County Commissioner Jeff Tobolski and multiple suburbs. Allies of Speaker Madigan have been circled by the feds. And Exelon and ComEd face a U.S. Securities and Exchange Commission investigation into the companies’ lobbying activities after the sudden retirement of Exelon’s top executive.

RECREATIONAL MARIJUANA LEGALIZED IN ILLINOIS

In June, Illinois joined 10 other states that have legalized recreational marijuana despite concerns about an increase in stoned drivers and the message legalization might send to the state’s children.

“In the past 50 years, the war on cannabis has destroyed families, filled prisons with nonviolent offenders and disproportionately disrupted black and brown communities,” Gov. J.B. Pritzker said as he signed the bill into law.

Marijuana has remained illegal despite all of the research and evidence showing it’s “safer than alcohol,” Pritzker said.

But as Illinoisans soon learned, the law — which takes effect Jan. 1 — doesn’t mean folks can light up wherever they want; nor can they head to the local convenience store to pick up weed along with a jug of milk.

For now at least, marijuana will be available at just a handful of locations in the city at specially licensed dispensaries. Naperville has banned the sale of pot within city limits — although city council members were considering putting the issue before voters.

And if you’re a visitor hoping to light up in your hotel room, think again. Many hotels are planning to stick to their strict no-smoking policies.

TWO MEGA DEVELOPMENTS COMING TO THE CITY

An Amazon headquarters may not be coming to the city, but two mega developments got the green light after the City Council in April OK’d a total of $1.6 billion in subsidies for Lincoln Yards and The 78.

The City Council approved the funding — the two biggest tax increment financing subsidies in the city’s history — in the waning days of Mayor Rahm Emanuel’s term, and after a late-night reversal by then-Mayor-elect Lori Lightfoot.

Lightfoot had called for a delay in voting for the subsides, which Emanuel had agreed to, but then changed her mind after saying she’d negotiated a deal with the developers of both projects to “meaningfully strengthen” their joint commitment to minority contracting.

As the Sun-Times’ Fran Spielman noted, it likely saved the mayor-elect from an embarrassing defeat because aldermen were poised to approve the subsidies without her support.

Work is under way on both projects. Lincoln Yards, a $6 billion project, is expected to bring a community of offices, residences and a hotel to the North Side along the Chicago River. The 78 — so called because developers say it will add to the city’s 77 current neighborhoods — will bring commercial and residential development to a long-vacant area near the South Loop.

Contributing: Jon Seidel