The fate of Tony Stark in Avengers: Endgame was planned long before cameras started rolling, as the Russo brothers have revealed that they learned about the death of Iron Man three years before filming began.
Avengers: Endgame ends with an alliance of almost every superhero in the MCU and their allies facing Thanos and his army. Thanos almost manages to seize victory with the Infinity Stones, but Tony Stark manages to use them first to destroy Thanos and his forces, which results in his own death. The fate of Tony Stark represents the culmination of a storyline over a decade in the making, as the carefree and selfish person from Iron Man performs the ultimate sacrifice for those he loves.
The death of Iron Man and the exit of Robert Downey Jr. from the MCU was not a recent decision. Anthony and Joe Russo recently participated in a Reddit AMA, where they answered questions about Avengers: Endgame, the MCU, and other projects that they will be working on in the future. The Russo brothers were asked how long ago they knew when Tony Stark was meant to die in Avengers: Endgame and the response from Joe Russo was "We knew for about three years before we shot the film". The Russo brothers were also asked about the most difficult day of shooting on Avengers: Endgame and their response was "Tony Stark's death."
Avengers: Infinity War and Avengers: Endgame were filmed back-to-back, with principal photography on both movies beginning in 2017. The filming of Avengers: Endgame concluded at the beginning of 2018. The Russo brothers would have learned about Tony Stark's demise at some point in 2014, which was during Phase Two of the MCU and predates the release of Avengers: Age of Ultron. 2014 was the year when Captain America: The Winter Soldier was released, which was also directed by the Russo brothers and they entered pre-production on Captain America: Civil War that same year. Phase Three of the MCU was kicked off by Captain America: Civil War, so the Russo brothers had the chance to prepare for Tony Stark's demise well in advance of it actually happening, even though there were last-minute changes to the schedule.
The death of Tony Stark was one of the most important moments in Avengers: Endgame, as the hero that kicked everything off was leaving the series for good. It's clear that Iron Man's absence and the departure of Robert Downey Jr. was not a decision that was made likely, nor with malice, and the directors who were responsible for handling his passing were given as much time as possible to prepare and do it right.
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