1. Secret Invasion
One of Marvel's most paranoia-inducing events, this Invasion of the Body Snatchers-style storyline sees some fanatic Skrulls under the rule of the charismatic extremist Queen Veranke invading Earth, replacing key superheroes with Skrulls, and sowing seeds of destruction and distrust among them, seeking to eventually take over the world.
With Skrulls coming in on the tail end of Phase Three in Captain Marvel's highly anticipated solo film, elements of this film coming true in the MCU seem more and more likely. It seems that Fury discovering the presence of hostile alien forces hiding on Earth is being hinted at already, with their secrets and trust being compromised by Veranke's Skrulls, whose rituals allow them to completely duplicate a person's memories and personality - making them even more dangerous than the other shapeshifters of their race.
Still, an entirely separate event in which Marvel's heroes have to contend with a full on, "Who will you trust" invasion, with calamities and events either happening concurrently or orchestrated by Skrulls within their ranks, would make for an amazing single-season TV series, if not its own full film.