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Ship or not, John is Bob’s second closest Thunderbolt after Yelena:
Despite his initial animosity, John seemed genuinely concerned when Bob sacrificed himself to distract the special forces from pursuing the trio. He ignored Ava’s instructions to leave, waiting for Yelena to say.
Aside from Yelena, he was the only one who faced Bob’s dark essence before the final battle (Bob probably also saw what was going on in his mind).
Despite seeing John as a complete ass, Bob treated him far more gently in the fight than he did Bucky and Alexei, though John was just as aggressive as they were (attacking, shooting).
He was the one who encouraged Bob and who praised him.
He was also the first to rush to help Yelena restrain Bob, despite having been impaled by a piece of iron just a minute before.
When John learned that Bob’s abusive father used to call him “Bobby”, he stopped doing it.
Other little thing: John was the one who freed Bob and saw his capsule in its opened state.