One of the key background story points that makes Tony Stark a.k.a. Iron Man (Robert Downey Jr.) who he is is the fact that he — much like D.C.'s Batman — is a wealthy orphan genius. Iron Man lost his parents in what he thought for years was a tragic car accident, and things have never been the same. He's been left to run his family's tech company, Stark Industries, and he's also used the tech to turn himself into Iron Man.
The death of his parents has affected his personality, and not only his own superhero narrative, but also the whole Avengers narrative. It's obvious early on in his playboy ways and his lack of friends that the death of his parents has left Tony with some serious intimacy issues. And based on his reaction to his vision from Avengers: Age of Ultron, he also doesn't handle loss, or the very thought of loss, very well. His paranoia of losing loved ones is what made the Sokovia Accords possible, and is what started the civil war between him and Steve Rogers a.k.a. Captain America (Chris Evans).
But Captain America: Civil War was a turning point for the Avengers not only because of their disagreements regarding having their operations approved by the U.N. A huge revelation was made close to the end of the movie, when Helmut Zemo (Daniel Brühl) answered the question that's been haunting Stark all his life.
In the wake of Age of Ultron, the place that accrued the most damage was a Central-Southeastern European country called Sokovia. And among those whose families were affected was that of Zemo's. Because of this, the villain made it his mission to have his revenge on the Avengers by making sure to tear them apart by having them destroy one another. His ultimate weapon of choice? A surveillance video of what really happened the night that Howard and Maria Stark died.
After successfully trapping Iron Man, Captain America, and Bucky Barnes a.k.a. the Winter Soldier (Sebastian Stan) all in one place, he rolls the tape showing that Stark's parents didn't die because of a car accident. It was Cap's good ol' friend Bucky who actually killed the CEO of Stark Industries/founding member of S.H.I.E.L.D. and his wife.
During the time of the assassination, Barnes was programmed to be a killing machine known as the Winter Soldier, under the command of HYDRA — an authoritarian terrorist group who want nothing but world domination. The organization sent the Winter Soldier to intercept a car, retrieve a package, and kill whoever was inside the vehicle. This was all because HYDRA knew that the Starks' car was transporting vials of Super-Soldier Serum, similar to the serum that gave Captain America his powers. Because the original formula used on the Cap's been lost, it's been a seriously long arms race between HYDRA and S.H.I.E.L.D.
As if the truth of how his parents died wasn't hurtful enough, Iron Man also finds out that his friend Captain America knew about it all along. This, of course, led to quite the action-packed throwdown among the three — with the Cap defending not only himself, but also Bucky. This also ultimately caused a huge rift between Stark and Rogers.
But in the comics, it's a completely different story altogether. Yes, there was a car crash that occurred, but the suspects for the staged accident don't even exist (or at least, not yet) in the Marvel Cinematic Universe. There's V-Battalion, a secret society formed during World War II to help fight the Nazis. Howard Stark was believed to be a member, but he betrayed them and they orchestrated his death. Another suspect in the graphic novels is the Roxxon Oil Company, which may sound familiar to Marvel fans as it's a main player in the plot of Freeform series Cloak & Dagger.
Endgame spoilers ahead. Tony has always had a complicated relationship with his relatively distant dad, but he's still felt his loss for most of his life. So the Endgame scene where he meets Howard before Tony is even born gives him an opportunity to get some out-of-chronological-order closure. The end of that story is tragic, but at least Iron Man knows how much his parents loved him.