The coach was forced to settle for his second-choice transfer target after arriving at Bayern, but still pulled off one of the most controversial deals in history.
In the majority of transfers, all three parties are made aware of any agreements in the deal. But that was not the case when Gotze, once dubbed "the talent of the century" by Matthias Sammer, made the switch across Germany's Klassiker divide.
The seeds of his controversial move were sown in March 2012 when he signed a contract binding him to Jurgen Klopp's side until 2016. "Everyone knows how comfortable I feel here," he said at the time. "The club are far from finished with their recent resurgence. And I want to be a part of it."
The words seemed somewhat less convincing when details emerged of a 37 million euro release clause in his contract. Amid the hustle and bustle of Dortmund's subsequent double win and Gotze's ongoing injury problems, the story was swept under the carpet. But Bayern had taken note.
Fast forward to December that year and Bayern was well on the way to securing domestic dominance. But it seemed the then 20-year-old had no intention of leaving. "We are not thinking of a move in 2013," his agent Volker Struth said.
At the time Bayern was working on securing new coach Pep Guardiola, whose arrival at the club was to be confirmed in January. He had a one-name wish list, Neymar of Santos, but the Bavarians' senior management disagreed due to their past problems with "young Brazilians". So they settled on the next-best choice - Gotze.
In the spring of 2013, the transfer rapidly began to gain momentum. Shortly after the 3-2 win over Malaga, Gotze's entourage informed Dortmund that he had agreed terms with Bayern.
"[Sporting director] Michael Zorc walked around the training ground as if someone had died," Jurgen Klopp reflected. Dortmund's approval was not needed and the club was powerless to prevent its most prized asset from leaving the club.
The public heard of the transfer some time later, but another intriguing story in the Bundesliga broke at the same time. On April 20, Munich-based magazine Focus revealed that Roten president Uli Hoeness was being investigated for tax evasion. Intense media scrutiny followed, but the former West Germany star refused to resign his position.
|A LONG TIME IN FOOTBALL
Timeline of Gotze's move
||Agent informs BVB of move|
||Hoeness case breaks|
||Bild announce the transfer|
||Clubs confirm transfer|
||Gotze stars in Madrid win|
Two days later, Bild's story about Gotze's move had broken and BVB had no choice but to confirm it the next morning, on the eve of the club's Champions League semifinal with Real Madrid, providing a convenient smokescreen for the Hoeness story.
"It could have happened at a worse time. Like four hours before the game," Klopp joked at his pre-match press conference. "But on a scale of one to 10, this is a nine." He also issued a plea for Dortmund fans to get behind the whole team, even Gotze, in the match.
It clearly worked. Dortmund won 4-1, with Robert Lewandowski scoring all of the goals.
The return leg at the Bernabeu turned out to be Gotze's last game for the club and anger from the stands intensified. As BVB saw it, the club's academy graduate and best player was leaving for its most hated rival.
So what had turned his head? There was a sporting factor that contributed to his decision. "The reason Gotze is leaving? He's Guardiola's target," said Klopp at the first press conference after the deal was announced.
As well as being coached by a man who had won everything and carries a mystique and allure few others can match, there was a financial factor. Gotze and his agent picked up 7 million euros in fees between them upon agreeing the deal worth 10 million euros a year - more than double his salary at BVB.
His total cost could exceed 114 million euros, but the Bavarians had poached Sammer's "talent of the century" and also significantly weakened its rival in the process. The club believes it will prove a price worth paying.
After Klopp's side lost to Bayern in the Champions League final, it returned to Germany, with Gotze being greeted by a chorus of boos. The club's anger was compounded in November when Gotze rose from the bench to score the first goal in a 3-0 win for Guardiola's side at Signal Iduna Park.
What had seemed impossible a year ago to Dortmund fans had become a grim reality.