WARNING: The following contains spoilers for The Suicide Squad, now in theaters and streaming on HBO Max.
The Suicide Squad marks the return of Joel Kinnaman and Viola Davis as Colonel Rick Flag and Amanda Waller respectively, reprising their roles from 2016's Suicide Squad. However, the relationship between the characters has apparently soured in the time between the first installment and its quasi-sequel, which subtly implies a feud between them.
In Suicide Squad, Flag was Waller's most dependable asset, in charge of her band of supervillains and the means to explode their heads if they disobeyed orders. Granted, Waller ensured Flag stayed in line, manipulating him to fall in love with the Enchantress' alter ego, Dr. June Moone (Cara Delevingne). All the same, she prioritized his safety by threatening to execute the entire Squad if he came to harm.
Her concern for Flag's wellbeing is significantly reduced in The Suicide Squad, as his team is almost entirely slaughtered after Blackguard (Pete Davidson) sells them out to the Corto Maltese military. Waller may or may not have anticipated this betrayal, but she nonetheless tells Flag's crew to battle the entire army, looking noticeably pleased when the inevitable massacre allows Bloodsport (Idris Elba) and his group to infiltrate the island undetected.
This is not to say that Waller wanted Flag to die, as she goes out of her way to have him rescued by the surviving Task Force X members. Nevertheless, he became far less useful to her when the Enchantress was destroyed and June was saved. As she told Bruce Wayne (Ben Affleck), "You believe in friendship. I believe in leverage." Without said leverage over Flag, she is entirely dependant on his willingness to carry out her commands, which is no guarantee given his change in attitude between movies.
Kinnaman himself has called Flag in The Suicide Squad "a completely different version of the character," who is "less cynical of the world and a little bit more idealistic." The first film's Flag barely flinched when Waller murdered her own aides to cover her tracks, saying, "I buried a lot of mistakes too." His borderline sinister detachment, heightened by the implication that he has committed similar crimes, made him closer in spirit to Waller, increasing his value on her ethically questionable operations.
Contrastingly, he expresses his weariness of burying such "mistakes" in the second installment, after the horror of discovering that the American government was behind Project Starfish and the resulting experiments on children. He takes a hard drive containing the project's records, intending to reveal all to the press, but is held at gunpoint by Peacemaker (John Cena), whom Waller explicitly charged with ensuring the records were destroyed. Flag's rebellion against his boss ultimately costs him his life, as Peacemaker kills him to get the hard drive.
Waller deploying a "backup" suggests that she anticipated Flag disobeying her. They were far from friends in Suicide Squad, but his bleaker outlook and concern for June kept them on the same page. During whatever missions occurred since then, Waller must have unintentionally nurtured Flag's desire to help the world, perhaps as penance for his shady past. The resulting distinction between serving his country and serving humanity is something Peacemaker has yet to consider, meaning he is still in a similar place to where Flag was years before.
In other words, Peacemaker has replaced Flag as the person who will carry out Waller's demands without question, despite being clearly unhinged. Whether or not it was instigated by a singular incident or a gradual decline, the opposing perspectives of Waller and Flag resulted in their working relationship breaking down, and without a bomb in his neck, she needed another way to take him out if necessary. In his tragic death, Rick Flag became like everyone else in The Suicide Squad: another pawn on Amanda Waller's board.
To watch Amanda Waller at her worst, see The Suicide Squad in theaters and on HBO Max now.