Major spoilers for Captain Marvel ahead. Well, you've done it. You've seen Captain Marvel and you probably 1) can't get enough of it, and 2) have some questions. It does a great job of being a unique stand-alone origin story, but it fits in to the Marvel Cinematic Universe in a way that might be a bit perplexing for some. There are of course Easter eggs for the MCU and other films (thank you, Ronan The Accuser, Nick Fury, and Coulson), but from the surface it might be hard to track how Carol will fit in with Avengers: Endgame. Especially since the end-credit scene and the newest trailer for Endgame hint that she'll be teaming up with the Avengers to take down Thanos, it begs the question: Where has Captain Marvel been since 1995? While there's no definitive answer yet, as it will most likely be explored in the next MCU film, there are some clues and ideas about where the character has been this whole time.
The last time fans saw Fury alive was in Avengers: Infinity War. He played a pivotal role, even if he wasn't on your screen for a long time. After Thanos' snap, and the disappearance of half the universe including a lot of the Avengers, the end-credits scene shows that Fury and Maria Hill were also taken out by Thanos' power move. Right before he's gone for good, Fury uses his intergalactic pager to call Carol Danvers back to earth to help the remaining Avengers. And considering there are over 20 MCU movies thus far, with Captain Marvel just now being introduced, fans can't help but wonder how she's existed through all of the movies, yet has never shown up.
1. Helping The Skrulls
So, a lot of people took issue with the fact that Captain Marvel is just coming into the fray in the year 2019 when she's been a super-powered human/Kree that S.H.I.E.L.D. has known about since 1995. However, being the strongest Avenger comes with its responsibilities. As we saw at the end of Captain Marvel, she offered her help to aid the Skrulls and find them a new home. She also made it clear that she wanted to continue Lawson/Mar-Vell's fight to end the Kree/Skrull war.
Trying to relocate a whole species of beings, plus trying to take out the Supreme Intelligence, and inform the Kree about who's the real enemy (if they didn't already know) is enough to keep anyone busy, even a superhero.
2. Working On Other Missions In Other Galaxies
We know that she took this mission in space to help out the Skrulls, but she could also be doing other missions in addition to this. There's a hint that the Kree/Skrull war was finished, with Ronan the Accuser working on a different motive by the time viewers see him again in Guardians of The Galaxy, which happens after Captain Marvel in the timeline. With that radical Kree out of Captain Marvel's hair, she could have defeated the Supreme Intelligence and is using her superpowers to bring peace to other parts of space as well.
In fact, in an interview with i09, Marvel Studios President Kevin Feige gave a very early hint where she could have been this entire time, "The key is…out there," he said, and i09 wrote that he sort of gestured to the air. Does this mean "out there" as in outer space? Or is he just being cryptic as he has to be with MCU projects, and just saying, "Yeah, she's been around"?
3. She's Been Out Of The Pager's Range
In addition to her very busy schedule fighting outer-space warfare, she also might just be too far away for Fury's pager to get a hold of her. Feige pointed this out to /Film in a recent interview. "How do you know he never hit it?" Feige said. "How do we know he never pushed it before? We've never seen him push it before. That doesn't mean he never did."
As the interview noted, that's a pretty good answer. In the scene where Carol and Fury are washing dishes and she bestows the high-tech pager to him, she mentions that it should reach a couple galaxies away with its range. But the Skrulls need to get pretty far away from the Kree to make sure they don't pose a threat to them anymore (which is why Mar-Vell was working on an engine that used the Tesseract's energy, which would most likely boost their travel distance). Since Carol was using her energy to be a conduit for said engine, she's probably pretty far away from C-53 (aka Earth), so she might not have heard Fury's ping if he did reach out to her during the Battle of New York or when Ultron wanted to wipe out all of humanity.
4. Fury Just Left Captain Marvel Alone
Whichever way you look at it, the reason we haven't seen Carol before might just be that they hadn't planned for the character to be included from the beginning. So from a production standpoint, they couldn't have hinted at her because it wasn't known since day one of Marvel Studios. But, even if that's the case (which it might not be), the last major option as to where she's been for the past 20+ movies is just that Fury hasn't called her because he didn't feel like he needed to just yet. In that same interview Feige did with /Film, he posited this: "...She does say it's gotta be a real emergency, right? Yeah."
You can of course make the argument that yes, a huge alien force as big as the Chitauri or advanced A.I. that wants to destroy every single human for the peace of the universe are major emergencies. But this is why Fury called in the Avengers. The whole point of creating the "Avengers Initiative" was to have a task force of super-powered individuals to defend Earth. What would have been the point of calling in Captain Marvel when the sole purpose of the Avengers is to defend in her place (even if they didn't know she was the catalyst yet).
So it would make sense that it's not until he's literally disintegrating that Fury calls in Captain Marvel. The other big conflicts that involved the Avengers thus far have been resolved on their own, and having a major trick up their sleeve, something only a handful of S.H.E.I.L.D. agents even knew about, is really going to work in their favor against Thanos. Whatever route they take to defeat him or bring their friends back, if you saw the way Captain Marvel obliterated a dozen (or more) warheads and just ripped through a fricken' spaceship, you can bet Thanos is a dead man.