However, five years into the future, during the time heist, we learn from the Ancient One that the Infinity Stones are essential to the flow of time. Removing the Stones from the timeline or worse, destroying them could shatter the very fabric of reality. But how could this be? If the Infinity Stones are essential to the flow of time and Thanos destroyed the Infinity Stones in the prime timeline, wouldn’t the be universe be in complete chaos? Well, as it turns out, the stones weren’t destroyed after all, not completely anyway. In an Endgame fan Q&A at the Smithsonian Air & Space Museum, the Russo brothers were asked about the Infinity Stones in the prime timeline. They had this to say:
This explanation does make sense. Thanos reducing the Infinity Stones to atomic level would prevent the Avengers from using them, while still keeping the power of the stones alive in the universe. But I can’t help but why the Russos didn’t at least include a line containing this bit of information in the movie. Why didn’t Bruce Banner question the Ancient One when she told him that the stones are essential to the universe? Having said that, from a storytelling point of view, it’s easy to see why the Russos along with screenwriters Markus and McFeely chose to omit that detail from the movie. Had the likes of Bruce Banner or Tony Stark actually realised that the Infinity Stones still exist in their timeline at an atomic level, they probably would’ve worked on locating the powerful gems and converting them into their physical form again, as opposed to going on an adventure through time. Then how would we get all the tear-jerking callbacks? (Source: Joe and Anthony Russo via zachzhou630)