Lex Luthor is now President of the USA (either he never became outed as The Boss of Metropolis nor tried to marry Lois *OR* the resurrected-soup Luthor ran years after being pardoned-by-a-clone-President Garner). His communications director is his ex-wife Arianna Carlin, who got him elected by issuing press releases that use subliminal messages that turn U.S. citizens into Luthor's adoring fan-base as well as against Superman. (The situations of Madame Ex did not happen in this timeline, so she and her tactics are unknown.)
Kryptonite is legal and sold in gun shops in bullet form, just in case New Kryptonians return to invade Earth again.
Lex Luthor issues an all out war on News as he believes that members of the press are part of the opposition party trying to oust him from power.
Lois and Clark still work at the Daily Planet, are married, and have several children, the eldest of whom is a teenager. After their eldest (due to some super powers) catches someone tailing him/her home from school, Lois and Clark decide it's not safe for their family in the city. Clark takes his wife and children to hide out in the woods outside the city. On his return, Superman is shot out of the sky by one of Luthor's fan-base as he believes that Luthor asked him to do so. (Whether or not Luthor actually did should be a topic of debate within the story. Perhaps there's a live - hot - mic incident where Lex is overheard saying something about wishing someone would kill his political enemies.)
Luckily, the bullet only grazes Superman. Clark's able to land safely, but decides to return to his family in the guise of Clark, so he isn't shot again. Unfortunately, someone recognizes him as Clark Kent -- wanted News Reporter and lie spreader -- and shoots him in the middle of the street, where the event is captured on many a security and cell phone camera (as was Superman's fall from the sky). Clark is able to drag himself down into a nearby subway station, where he falls onto the tracks, again in full view of many a cell phone camera. Clark rolls away and runs down the tunnel just as a train arrives. Everyone thinks that Clark Kent was killed by the train.
Clark finally makes it out to woods to meet up with his family, only now he's a dead man (both as Superman and as Clark Kent).
Luckily, Clark has foreseen (predicted) the rise of Lex Luthor back in the 1990s and set up an alias for himself, Lois, and the kids. The Superman Foundation invested in an internet start-up company (thanks to the help of Jimmy), making the Foundation and the company's creator -- Charles Clark -- buckets of money when it was sold.
Charles Clark and his wife Lola Clark bought the old Kent Farm in Smallville, hiring Wayne Irig to run the farming. They use the story that the Clark family lost all their internet money in a bad investment and now have to move onto their 'retirement' / 'investment' property full time. The Kents are long since dead (possibly this is an alt-alt-universe, one where Clark's an orphan like alt-Clark, who was shipped off to relatives out west, so he never got involved with Lana before he moved to Metropolis like canon Clark, and rest is history). Lois and Clark hadn't been back to Smallville since the incident in 1993 (GGGoH), where Clark re-acquainted himself with Wayne Irig.
Now, Lois and Clark (Charles & Lola?) need to raise their children (they debate whether to homeschool their kids or send them to Smallville public schools, which are filled with children of loyal Luthor supporters), all while trying to stop Lex Luthor from destroying their country or discovering where they are and finishing the job.
Lois -- as a blogger -- is on the forefront of people calling for President Luthor to be tried for inciting violence by encouraging his followers that those in the press were 'the enemy'. Perhaps she and Clark discover Arianna's brainwashing techniques and reveal her tactics to the world.
Do these things bring down the House of Luthor or just shine the spotlight on the Clark family? Can Lois and Clark ever return to their old life, or are they stuck Smallville, trying to raise their super family in secret?
