How Mar-Vell Was A Skrull All Along In Captain Marvel
So Captain Marvel decided to throw a few twists into its plot. One of these twists dealt with Mar-Vell, Captain Marvel’s mentor figure. Actually, a few of the twists dealt with Mar-Vell. For one, Mar-Vell ended up being a woman rather than a guy like in the original comic. Two, Mar-Vell is not the reason Carol received her powers -- at least, she’s not the direct reason. In the comics, the explosion of the device called the Psych Magnetron splices Carol’s DNA with that of Mar-Vell’s. Now bonded with his Kree DNA, she naturally has access to Mar-Vell’s powers.
In the film, while Mar-Vellis still a Kree and Carol still receives her powers from an explosion, neither are related. The explosion that gives Carol her powers is powered by the Tesseract, which in turn is powered by the Space Stone, making Carol similar to Scarlet Witch in origin. All of this is to say that Mar-Vell and his role were completely reworked for the premise of the film and considering the other twists that the film had to offer, who’s to say that Mar-Vell couldn’t also have actually been a Skrull in disguise.
The Skrulls
Being competent, Captain Marvel marketed itself in a way that made you think the Skrulls were the bad guys of the film, only to turn this concept upside down on its head by the end of the movie’s second act. It turns out that everything Carol had been told since being taken from Earth, was a lie. The noble hero warriors that she looked up to at the beginning of the movie actually happen to be psychotic, warmongering narcissists who only want to enforce their will on the galaxy. If you’ve seen any of the MCU movies, this probably didn’t come as much of a surprise at all since it reflects Ronan’s main motivation in the Guardians of the Galaxy movie.
The Skrulls are actually the victims and not the aggressors here. They just want to be left in peace. Mar-Vell creates the light-speed engine as a way to help them. It’s something that the Skrulls can use as a means to escape the Kree. Considering how there wasn’t a single Kree that was actually a good guy in the movie, maybe that means Mar-Vell wasn’t either. Maybe due to the Kree overpowering them, the Skrulls decided to do what they do best and infiltrate their planet, taking on guises in order to fit in with the ranks. Mar-Vell just so happened to be an identity that the Skrulls decided to take on.
Mar-Vell’s work eventually leads her to Earth where she found out about the Tesseract and tried to engineer some type of salvation with it. It had already been used to create super-powered weapons so why couldn’t she use it for something more passive? However, at some point, the Kree found out what Mar-Vell really was. They could have killed her sooner, but when they discovered that she was creating an engine that could achieve light speed they decided to let things play out and finish her after everything was said and done. Before they could take the engine from Mar-Vell, however, Carol destroyed it, becoming infused with the powers of the Space Stone in the resulting explosion. When the Kree saw that Carol was still alive, they figured that all wasn’t lost and decided to go ahead and kidnap her and use her as a weapon against the Skrulls.
Goose
Another sign that Mar-Vell might be a Skrull could rest with Goose. Goose is Flerken an alien species that has the appearance of a cat. Goose’s original owner was Mar-Vell. She lived on after her master's death. Mar-Vell knew what Goose was. She was more than likely the reason Goose was on Earth in the first place the Flerken was her pet. However, the Kree soldiers, when they invaded Mar-Vell’s during the climax, needed a machine just to tell them that Goose was a Flerken. Talos on the other hand, a Skrull, knew exactly what it was just by sight, same as Mar-Vell.
Mar-Vell
Captain Marvel doesn’t dive too deeply into Mar-Vell’s background; she’s given somewhat of simplistic summary. She’s a Kree scientist who happened to find herself on Earth. At some point, she defected from the Kree and tried to help their enemies in the Skrulls. The Kree found out about it, and then they killed her. We don’t get much else than that. In the comics, Mar-Vell was sent to Earth in order to keep an eye on the planet's space-traveling capabilities, but in the end, decides to betray the Kree in order to keep Earth safe from them. We can assume that the Mar-Vell of the MCU was in the same boat, but considering everything else about her seems to have been tweaked in some way shape or form, it’s hard to imagine things looking like they did in the comics.
We have no idea why Mar-Vell was on Earth. Perhaps it was to make sure that Earth didn’t have any prevalent space traveling technology. Her lack of a detailed past seems pretty suspicious all things considered. Her role is also pretty lackluster despite her being someone who’s supposed to be a major influence on Carol’s life. With that being said, maybe she’s isn’t dead after all -- a pretty big waste of character if she happens to be. There seems like so much more that could be done to develop her relationship with Carol.
From the way things played out in her death scene, she probably isn’t dead. The moment, Yon-Rogg shot her in the chest there was never really any dramatization over it. She’s shot and then the scene focuses on Carol and Yon-Rogg. So maybe after Carol passes out from the explosion, Yon Rogg takes both her and Captain Mar-Vell back with him to Hala. Mar-Vell is revived and told to build the Kree new light speed engine. She refuses for some time but ends up breaking after a while, informing the Kree that the only way she can complete the ship is if she has the Tesseract core.
This could explain how Yon Rogg knew about the core despite not having any interactions with Mar-Vell after shooting down her plane, opting to immediately put a round in her chest instead. His original mission also had nothing to do with Earth. He seemingly only went there because Carol had reached out to him and told him of where she had crashed landed. So it’s possible he took on the mission of nabbing up the core after realizing he had to get Carol back anyways.
At the end of the movie, Carol spared Yon-Rogg and sent him back to Hala with a threatening message. She then took it upon herself to help the Skrulls find new homes and survive the Kree. She’s been gone for over two decades, so it’s possible that’s she’s already invaded Hala and discovered Mar-Vell there (assuming of course she’s still alive). After learning that Mar-Vell is a Skrull and not a Kree, Carol opts to fulfill her promise of finding her a new home. This adventure could even be the bases behind any Captain Marvel sequel that may come out in the future.