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I've worked with the baseline of this scenario in another forum, would be interested in discussing it.
Around 1978, the relationship between CDU and CSU parties worsens, leading to a split between the political factions in the German parliament.
Subsequently to this split, regional patriotic feelings are stirred in Bavaria and other South-German states
Around 1979, CSU becomes active in other South-German states
In 1981, a motion is set to form a new, third state in South Germany, consisting of North Baden, and parts of Württemberg, Hesse and Rhineland-Palatinate
Starting in 1982, the CSU internally becomes somewhat more supportive of separatism and starts adopting an anti-federal stance
In 1983, the new third state is created through a referendum, with moderate positive approval in the population.
By 1986, regional separatism in the three South-German states has gained considerable approval ratings
In 1987, several states in "North Germany" are reformed and combined through a series of referendums which while succeeding have some impact with local patriotism forming there as well.
F.J.Strauss, charismatic leader of the CSU, does not die in 1988, but survives until at least 1991
In 1988, a major political collision between North and South Germany occurs when South German states blockade an increase of (Cold War) Military Spending in parliament
Following that, political deadlock in lawmaking occurs consistently throughout 1988 and 1989
In late 1989, real events in the German Democratic Republic occur
Political deadlock prevents the German Federal Republic from absorbing the German Democratic Republic
2+4 and similar post-Cold-War treaties are delayed somewhat
Separatist southern lobby groups actively undermine the Federation in North and East
In 07/1990, the separatists see a first success in East Germany declaring it will continue to remain independant
Between 08/1990 and 12/1990, more or less openly separatist factions win elections in all three South German states, with blatant separatist "rebel" stances adopted by the new state governments
In 02/1991, Bavaria declares itself independant of the German Federation
In 03/1991, the other two states follow
In subsequent treaties signed 05/1991, occupation powers bail out of the increasing quagmire of now 5 states as fast as possible
Personal rapport (Strauss/Gorbachev) and political scheming see to limited support of the Soviet Union and France for the separatists especially in the 1988-1991 period
Is this so far not too far-fetched? Trying to keep some semblance of "possible" in there.