Only seven days ago, things were looking pretty good. Bayern was 10 points clear, dominating the Bundesliga and cruising to a record title.
It had a German Cup semi-final against Borussia Dortmund to look forward to, while preparing for another UEFA Champions League quarter-final in what seemed a favorable draw against Porto.
Fast forward seven days, and it’s a very different story.
A demoralising 3-1 defeat away to Porto in the UCL was swiftly followed by the news that legendary club doctor Hans-Wilhelm Muller-Wohlfahrt was resigning after 40 years in the role, claiming the club's medical department was blamed for the shock defeat.
Muller-Wohlfahrt is someone I know very well from my time in Germany. He not only looks after his Bayern players and the Germany national team, but athletes from all over the world, like me, even though I was playing for a rival club.
He has a reputation for being a leader in sports medicine and I experienced his pedigree first hand when I tore my hamstring in 2000.
I went to see the famous doctor and he injected me with a special natural medicine which accelerated the recovery. Incredibly I was back much quicker than more common, conventional treatments.
A few years later I played in England and the technique was only starting to be introduced there. He is well ahead of the curve.
Pep later clarified that only the manager is to blame for a defeat during a news conference, but reports in the German media suggested chief executive Karl-Heinz Rummenigge and Muller-Wohlfahrt had clashed over the huge injury-list, which includes Arjen Robben, Franck Ribery, Medhi Benatia, Javi Martinez, David Alaba and Bastian Schweinsteiger.
Either way, the medical staff has cleared out, while the concerns over the injury-hit squad and Bayern's UCL campaign remain. Now the question is can the German giant turn it all around and pull off a remarkable comeback?
Pep's brilliance remains unquestioned from what he achieved at Barcelona and what he has done in nearly two years with Bayern. Yet it is only in the Champions League where he can cement himself as a genuine great.
Last season Bayern destroyed everything in its path, breaking record after record, but then became a victim of its own success.
Having wrapped up the Bundesliga title at a canter, the pressure was taken out of the remaining fixtures and it started to look flat.
Just when it needed to be at the top of its game again, Bayern proved way off the pace and lost 5-0 on aggregate to Real Madrid in the one-sided Champions League semi-final.
After the loss to Porto midweek, Franz 'der Kaiser' Beckenbauer pointed out, 'Bayern Munich stars played like they were on sleeping pills' and 'Dante looked like he was wearing 'ski boots'.
It wasn't a ringing endorsement for a player who had so impressed his coach just days ealrier against Borussia Dortmund, prompting Pep Guardiola to say he would "like 1000 Dantes in my team."
A series of clangers in the days that followed would be enough to leave the Spanish coach wishing he didn't have one.
While Bayern has an incredibly talented squad, its depth has been tested and when a side is missing the likes of Ribery, Robben and Schweinsteiger it is glaringly obvious.
I don’t think anyone expected the shocking defensive display we saw in Portugal last week or the drama which unfolded in the days afterwards.
But, as Dante has comically proven, a week in football is a long time.
So hopefully for Pep and Bayern, just as quickly as what was shaping up to be a magnificent season steered off track, this prodigious coach can get his immensely talented squad back on the road to greatness.
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