The ‘MCU Phase 5’ series ‘Secret Invasion’ can justify the ‘Captain Marvel’ twist that depicted the Skrulls as the good guys. Captain Marvel's infamous Skrull twist irked many MCU viewers who were familiar with Marvel Comics' Kree-Skrull War and "Secret Invasion," which originally portrayed the Skrulls as a spacefaring empire that is just as bad if not worse than the Kree. However, the MCU movie might have just been setting up the best possible long-term story arc for the Skrulls - not just in Secret Invasion, but throughout the entire MCU Phase 5 slate.
The announcement of Secret Invasion in Comic-Con 2022 has rekindled the debate about which are the better Skrulls: the good ones from the MCU or the evil ones from Marvel Comics? In the MCU, Skrulls are refugees from a war that was started by the Kree, vilified by Kree propaganda as evil, shapeshifting invaders. Though the same can be said of Marvel Comics' Skrulls, the Kree's description of Skrulls is mostly accurate in the comics. Throughout the Skrulls' long comic book history, there were very few Skrulls who weren't actively malicious to those they encountered.
Secret Invasion can still stay true to how Marvel Comics depicted Skrulls, even without retconning anything from Captain Marvel or anywhere else Skrulls have already appeared. Considering everything that's already been established about the Skrulls, the MCU's Secret Invasion - Marvel Studios' first crossover event - has everything it needs to justify why Skrulls weren't evil in Captain Marvel. If Secret Invasion sees Skrulls fighting for and against Earth, then it might just settle the debate and prove that sometimes, the MCU can actually do it better than the source material.