The sun burned, Champions League hopes evaporated and all of a sudden the lightning rod for Arsenal supporters’ disillusionment moved away from the man in the dugout and out towards the Atlantic. The chant started in the North Bank and suddenly spread, growing in urgency as it coursed round the stadium: “Stan Kroenke – get out of our club.”

The news that broke last week about Alisher Usmanov’s $1.3bn bid for the majority shareholding held by Arsenal’s American investor has broadened the conversation about the club’s status and ambitions. While the disaffected have generally pointed their fingers at Arsène Wenger the club’s direction above and beyond the manager is now under scrutiny. Kroenke is expected in England next week before the FA Cup final. The microscope is not something he welcomes but the lens will inevitably focus in. The Kroenke model across his sports franchises tends not to reach for the stars and Arsenal’s fanbase want a say about that.

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The Wenger debate appears – for now at least – to have quietened. For all the huff and puff about the consequences of finally slipping out of the Champions League reckoning, in the end the mood around the Emirates was mild and accepting. There was not a hint from the home crowd there might be a final curtain any time soon for the manager who has called the shots for two decades. The impression was of a crowd expecting to see him back in situ for the Emirates Cup in July.

Wenger normally joins in the traditional lap of appreciation but this time he stayed on the sideline, watching from the edge of the pitch as his players waved and absorbed good wishes before Wembley. He thought it best to keep his distance just in case it was a bit of a distraction – and his players have had enough of that to deal with.

Play Video 1:01 Arsène Wenger takes responsibility as Arsenal fail to secure Champions League place – video

His downcast disposition after the match suggested that deep down he feels troubled that his proud record of consecutive Champions League qualifications is over, in terms of what it represents as a status symbol as well as the obvious lament that Thursday nights and far-flung travel are never ideal crammed into an already busy schedule. Round these parts they used mockingly to call them “Spursday nights” and now this is their domain.

Wenger said he felt sad and that it was strange to imagine life without the Champions League soundtrack. The last time Arsenal finished a league campaign without that particular prize was in 1997. Their final game was at the now-defunct Baseball Ground. The old double act of Ian Wright and Dennis Bergkamp scored the goals. As it happened, Manchester United finished champions with 75 points that season – exactly what Arsenal collected for this fifth-placed finish.

Wenger was candid in accepting responsibility. The storm clouds that accompanied the questions about his future were damaging. He said the psychological environment the squad had to deal with at the darkest moments grew “horrendous”. (Which begs the obvious question as to why he and the club were not able to sort out the contract and alleviate some of that pressure.)

Is a season outside the Champions League the end of the world? How critical is it in terms of keeping players whose contracts are winding down, like Alexis Sánchez and Mesut Özil, or attracting shiny new ones? Those conversations are on hold for another week, certainly until after the FA Cup final.

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They at least head into a rendezvous with the champions, Chelsea, on the back of some decent form – in beating an Everton side halfway to the beach they picked up a seventh win in eight games. But they have their worries, especially defensively. Laurent Koscielny will curse misjudging a challenge on Enner Valencia. He clattered clumsily through the Everton forward, was sent off and the chance to lead his team out at Wembley in the FA Cup final is scuppered. Gabriel Paulista then overstretched his knee and left the pitch visibly pained.

Wenger assessed the season and came to the conclusion that he did not feel his team were so far from building a stronger Premier League challenge. But all that instability and uncertainty he referenced as harming this one still needs resolution. It is some list: the future for Wenger, Sánchez, Özil, Alex Oxlade-Chamberlain, the returning Jack Wilshere, Wojciech Szczesny, various members of the backroom staff, the up-in-the-air director of football role in different name, head of youth development ... It all needs sorting even without considering where they might strengthen their squad.

“Forward Arsenal” used to be an old motto of the club and the sense of drift needs addressing. The battle for a club’s soul lurks in the background. It fluttered to the foreground with the chants in Kroenke’s direction, and the sense it will not easily go away persists.