It's official; even SHIELD don't know why Black Widow joined them. Although the upcoming Black Widow movie isn't an origin story, most viewers are expecting it to shine a light on Natasha Romanoff's MCU backstory. Until now, audiences have had to settle for a drip-feed off information, primarily through the Avengers movies, but that's surely about to change.
Black Widow is set shortly after the events of Captain America: Civil War, with Natasha Romanoff now one of the world's most wanted. This forces her to return to Budapest, where she recruits fellow (former?) Black Widows Yelena Belova and Melina Vostokoff, as well as the Red Guardian. It's reasonable to assume they were unknown to SHIELD, meaning Natasha's pursuers won't trace her to them. Incredibly, though, according to this week's Black Widow Prelude #1, that isn't the limit of SHIELD's lack of knowledge; they never knew why Black Widow joined them in the first place.
The Black Widow Prelude is set almost immediately after the main events of Captain America: Civil War, and before Steve Rogers had broken his allies out of the Raft. General Thunderbolt Ross is attempting to persuade the World Security Council to make the capture of Natasha Romanoff a priority, and he arranges a private meeting with Councilwoman Hawley. There, he recounts Natasha's history, and in one scene discusses how she came to join SHIELD. Incredibly, Ross offers three alternatives.
"One account is that she ran into Barton during a mission that went horribly wrong. He saved her life, and under the stress of the situation, they bonded. Another is that she saved Nick Fury's life, and he was so impressed by her that he offered her a position with SHIELD. It's also possible that the ceremony she underwent caused her faith in her homeland to deteriorate and she wanted a fresh start. All we know is, she became an agent of SHIELD."
It seems Ross and his agents have absolutely no idea how Black Widow joined SHIELD. In fact, the three theories that he presents are common among fans, suggesting he has no more of a clue than anyone who's watched the various Marvel movies. And that's actually quite remarkable, because it's important to remember General Ross has access to the old SHIELD databases, all of which were published online in Captain America: The Winter Soldier. He should know everything in Natasha's file; how she came up on SHIELD's radar in "the worst possible way," the exact circumstances of her encounter with Clint Barton in Budapest, and what intelligence she gave SHIELD on the Red Room.
And yet, General Thunderbolt Ross - the man in charge of implementing the Sokovia Accords - knows none of this. The analysts he's had working for him have drawn a blank. The only possible conclusion is that Nick Fury had Black Widow's history excised from SHIELD's records, in the same kind of way he removed any reference to Hawkeye's family. Fury considered Natasha Romanoff one of his best, and he protected her, so much so that just a handful of SHIELD agents even knew why Black Widow was now part of the team.
Black Widow Prelude #1 is on sale now from Marvel Comics.