The news has caused plenty of conspiracy theories to emerge, largely due to Goetze's pending transfer to Bayern for €37 million on July 1.
Whatever the cause—be it Bayern's command, Goetze's lack of will or the fact that he is actually finished for the season (most likely)—Juergen Klopp now has a big dilemma on his hands.
How will BVB organise themselves without Goetze?
The young German has emerged as one of the finest No. 10s in football and subsequently nailed down his place in the centre of Klopp's 4-2-3-1 formation.
The system isn't built around him, but BVB like to change their skin on a weekly basis and shift the focus of their play. The lack of Goetze doesn't hurt them in the way Lionel Messi's absence hinders Barcelona, but it strikes a line through one of several avenues of attack die Schwarzgelben utilise in game.
On paper, Klopp has three options.
Option 1: Introducing Kevin Grosskreutz
Grosskreutz is a polarising player.
It is undeniable that he was a key player for Klopp when Dortmund were rising to power, but since they've taken their perch at the top he's been frozen out to an extent.
He's made do with cameos and bizarre roles such as playing as a makeshift right-back, as the left-wing spot is now home to the figure of Marco Reus.
Some Dortmund fans have no issue with Grosskretuz coming in on the left and Reus switching inside, but others find this prospect obscene.
Option 2: Nuri Sahin In, Ilkay Gundogan Forward
The other viable choice is to keep Marco Reus on the left and push Ilkay Gundogan further forward.
BVB's No. 8 began his career as an attacking midfielder at Nurnberg, but was moved into defensive midfield by Klopp. He's become a fantastic No. 6, but has played in his old role against both Bayern Munich and Wolfsburg since Goetze went down.
Moving Gundogan forward leaves a hole at deep-lying playmaker, but Nuri Sahin can easily step in and play. The Turk has endured a poor 18 months at Liverpool and Real Madrid, but he still possesses the talent that saw him grab the headlines two years ago.
Playing Reus centrally is a gamble, and this way the template of the side stays the same.
Option 3: Back to the 4-3-3?
The 4-3-3 remains a viable formation for Dortmund, having used it at random points throughout the last two seasons.
This would likely feature a front three of Reus, Robert Lewandowski and Jakub Blaszczykowski, then a midfield three of Sven Bender, Gundogan and Sahin.
While it's strong on paper and the players are used to it, it leaves the Bayern holding midfielders unattended to and free to dictate.
Jose Mourinho failed to nullify for Gundogan in the deep-lying playmaker role and got burned for it—surely Klopp wouldn't make that mistake after watching his side prosper from it?
Which formation and starting XI do you see Borussia Dortmund taking?
Do you like the idea of Grosskreutz starting the final, or would you rather see Gundogan play as a No. 10?
Goetze is a big loss, but he's not irrecoverable—what would you do to solve the dilemma?
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