1973-1974
In an era in which they had to fight a young and energetic Borussia Mönchengladbach team, Bayern Munich managed to wrestle the trophy away from them by a measly one point. They managed to turn around a contest against Atletico Madrid in the final seconds in the European Cup thanks to a Hans-Georg Schwarzenbeck strike. Bayern went on to win the European Cup with a 4-0 victory in Munich. Yet, they failed to win the treble because of a rather fateful match in the DFB-Pokal semifinals.
Bayern had been drawn to play Eintracht Frankfurt. Frankfurt were certainly no minnows; they finished fourth in the league and both of the contests in the Bundesliga finished in draws (1-1 in Frankfurt; 2-2 in Munich).The game in the Pokal seemed to be heading the same way and seemed to be destined for extra time.
Bernd Hölzenbein gave Frankfurt a lead early in the second half; that lead lasted just more than ten minutes as Bayern equalized through Uli Hoeness. Two minutes after Hoeness' strike, Paul Breitner scored from the spot. Two minutes after Bayern's penalty, Frankfurt were awarded one but Jürgen Grabowski failed to convert. Yet, it took Frankfurt very little time to equalize. Less than ten minutes after Breitner's strike, Thomas Rohrback equalized for the Eagles.
However, as both sides went for it, Bayern's rather reliable defense made matters easy for Frankfurt. A penalty was awarded to the side and Jürgen Kalb, in the ninetieth minute, handed Frankfurt a berth in the final. Bayern, no strangers to conceding last second goals in vital matches, saw their hopes for the 74' Pokal come to an end in that April day. When May came, they held aloft two more important trophies but missing out on the little one meant that they would have to wait for the treble.
1998-1999
They should have come away with three but came away with only one. Leverkusen never even came close to challenging as Bayern won the title by 15 points. But their failings on one pitch in Barcelona led to their failings on another pitch in Berlin. The ribbons had been tied; Mario Basler had settled the final. Bayern would carry number four to Munich. Yet, in the most cruel of circumstances, Manchester United handed Bayern their second most (or even most, depending on where you stand) painful defeat in a Champions League final, scoring two in the final seconds. With the Pokal final scheduled in mid-June, Bayern had little time to recover.
They met a determined Werder Bremen side. Yet again, an early lead was to turn to dust. Yuriy Maksymov scored in the fourth minute but Carsten Jancker, then a Bremen star, equalized. The two teams could not be separated and the match went into penalties. Bayern converted the first four of their efforts while Bremen missed their second (Jens Todt). All Stefan Effenberg needed to do was convert from the spot. The most reliable of them all, the hard-liner, failed. Bremen were back. Yet, Bayern could have still won had it not been for Lothar Mattäus. He missed his chance from the spot. Bremen carried home the cup with the green jewels. And Bayern were left licking their wounds.
2000-2001
Matthäus had moved on by now, but Effenberg remained. He would inspire a comeback in the UEFA Champions League in the final. Bayern were not scared despite the events of the past two years ago; they wanted to win so badly though that they seemed to play to not lose rather than to win. The match went to penalties (1-1 after normal time) and after Oliver Kahn kept Valencia at bay, Bayern held the trophy aloft. In the Bundesliga, a last second free kick against Hamburg decided the title race in their favor instead of Schalke.
Yet, they failed in a rather bizarre contest against FC Magdeburg in the second round of the DFB Pokal. Bayern went behind to an Adolphus Ofodile goal but, with just over ten minutes to go, Hasan Salihamidzic equalized. The match went to penalties; once again, two very reliable players, Jens Jeremies and Giovane Elber, missed from the spot. Bayern were dumped out much too early from the Pokal and there is definitely reason to believe that had they overcome Magdeburg, they might have gone on to win the trophy.
2009-2010
The nearest and dearest of the treble misses is probably the 2009-10 season. Bayern reclaimed the league from VfL Wolfsburg and won the DFB Pokal final against Werder Bremen as well. The only contest they had left to win was a contest they were simply glad to be a part of. Bayern played their first Champions League final in nine years against Inter Milan and lost to a team which was better-prepared thanks to Jose Mourinho's nous. A defeat was acceptable, especially because this is the closest Bayern ever came to a treble before 2013.
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So, there you have it. The Pokal and some stoppage time shenanigans prevented Bayern from lifting the treble before 2013. When they ended up doing so in a very close final against VfB Stuttgart, the wait seemed to be worth it.