Liverpool lost their unbeaten record at Anfield, perhaps any realistic chance of European glory, probably the farewell so many envisaged. But that wasn’t all. “We lost the plot a little bit,” said Jurgen Klopp. The German can seem to write his own story. He had supplied the twist in the plot with the sudden announcement of his resignation. Now the final chapter is starting to look very different. The treble may become the single, the Carabao Cup Klopp’s last trophy. Three days after what may now be his last match, Atalanta could win the Europa League. This was not the script Liverpool wanted.

Instead of building to a climax, the danger is that Klopp’s reign peters out. They have lost a first leg in Europe 3-0 before and staged a stirring, stunning comeback, but Barcelona may forever remain a one-off. Anfield has been the scene of some wonderful European nights under Klopp, but an evisceration by Atalanta was probably his worst on home soil and definitely Liverpool’s joint heaviest in continental competition on Merseyside. After going unbeaten for 33 games at Anfield, the fortress was stormed by a side 32 points behind the leaders in Serie A.

“This was probably a low point for us performance-wise, I would say, for a long time,” said Klopp. “We can make this the shortest press conference.” He didn’t, though, instead delivering a damning analysis. “It was a really bad game: oh my God. A lot of performances tonight were really ‘oops, wow, I didn’t know they could play like that’. A lot of the players looked really alone in a lot of moments. It was really bad. “We were everywhere and nowhere. Midfield was spread like that, right midfield and left midfield, I didn’t recognise it a bit, it was really quite strange.”

The things Klopp might have recognised – a bold tactical plan, high-speed, high-quality counter-attacks, a well-coached team recording a famous win – instead came from Atalanta. The German rued his side’s inability to capitalise on the Italian side’s man-marking. “If you are in a better playing mood than we were tonight then you can cause massive problems but we didn’t,” he said.

Liverpool instead caused themselves massive problems: with two goalkeeping blunders from Caoimhin Kelleher, and a host of other errors. “Too many individual mistakes,” said captain Virgil van Dijk. “We were wide open but we lost the balls in difficult areas.”

But also with a series of misses, with Darwin Nunez responsible for the worst. And with Klopp’s team selection. He has been a master of perming the right combinations from a large group this side, or of rallying the last men standing amid injury crises. But making six changes would have made sense in a Europa League group stage, or with a 5-1 first-leg lead against Sparta Prague. To do so against Atalanta, however, suggested Klopp underestimated them or overestimated the back-up players who have flourished in other matches but floundered here.

Liverpool lacked their usual pace on the flanks, with Harvey Elliott and Cody Gakpo, neither noted for his speed. Neither remained in his starting position by the hour mark; Elliott was among a trio removed at the break when Mohamed Salah, Dominik Szoboszlai and Andy Robertson, three of the rested, were pressed into service. But there were defensive problems on either side of the pitch, too: Kostas Tsimikas was exposed for the opener and invariably out of position. On the right, Joe Gomez has lost form after a fine season. So, too, has Wataru Endo in the malfunctioning midfield.

“I am responsible for this result first and foremost, I know that,” Klopp said. “But the decision [about the starting line-up] would remain the same.” It is easy to attribute defeat to rotation whenever it occurs, but Liverpool lacked chemistry. “That’s how it is, we lose a game then it’s the changes… but I get the question, 100 per cent,” Klopp said. “One of the reasons I would do exactly the same again is if we want to be good in the rest of the season we have to make changes.”

The rest of the season now feels focused on the Premier League; with three of their next four games away from home, with points dropped at Old Trafford on Sunday, with momentum suddenly lost, Liverpool could do with the kind of response Klopp has secured many a time in the past.

And, indeed, with a show of solidity. If this was a shock result, there were warning signs. They now have no clean sheet in eight, three in 17 games in all competitions. They have been masters of escapology in other games but there is only so long a team can continue to get out of jail. Liverpool had made it to April unbeaten in all competitions at Anfield, despite trailing to Bournemouth, Leicester, Arsenal, Fulham (in two different competitions), Luton, Manchester City and Brighton. Atalanta, however, were the team who extended an advantage to 2-0 and then 3-0.

As a club, they have come back from 3-0 down to win a Champions League final against AC Milan. Under Klopp, they have recovered from a 3-0 first-leg deficit to win a semi-final against Barcelona. Even the author of that famous fightback, however, was not promising such a shift in the plot in the final pages. He added: “It’s not the moment for having a big mouth and telling them what we will do there.”