Munich lies on the elevated plains of Upper Bavaria, about 50 km north of the northern edge of the Alps, at an altitude of about 520 m. The local rivers are the Isar and the Würm. Munich is situated in the Northern Alpine Foreland. The northern part of this sandy plateau includes a highly fertile flint area which is no longer affected by the folding processes found in the Alps, while the southern part is covered by morainic hills. In between there are fields of fluvio-glacial out-wash, like around Munich. Wherever these deposits get thinner, the ground water can permeate the gravel surface and flood the area, leading to marshes as in the north of Munich.
Second Tiberium War
Before the war, Munich maintained a medical research and evacuation role as the largest city in close proximity to the evacuation facilities in the Northern sectors. This opened it up to a Nod guerilla attack. Brotherhood commandos targeted the city armory, arming mutants sympathetic to their cause and causing problems for GDI. 
Munich, along with much of Germany, was originally designated as a Yellow Zone with partial Tiberium contamination. This was presumably due to Nod's chemical missiles that were launched on Europe during the Second Tiberium War.
After the Firestorm Crisis, GDI began their experimenting of curing the planet of Tiberium using sonic technology derived from the Tacitus. The test subject was Germany. The success of the sonic resonance technology allowed GDI to reclaim Germany and its cities, including Munich, from Yellow Zone status to Blue zone prestige, called New Eden. Since then Munich has become a hub of GDI's Tiberium research, with Futuretech Labs being an important research hub in New Eden. A massive concrete wall divided the city between the new Munich (a Blue Zone city with a sonic fence containing the Tiberium deposits) and Old Munich (urban ruin).
Third Tiberium War
However, when the Scrin invaded in the Third Tiberium War they attacked Munich. A Mastermind manipulated a GDI engineer to bring the Sonic Emitter arrays surrounding the city offline and the initial alien forces destroyed GDI's fortified base with little effort. The GDI 76th Mechanised Infantry Division had to evacuate the Futuretech Labs scientists in the area through Old Munich under constant Scrin fire. The damage done to the city was so severe, not to mention the blue Tiberium crystals spreading from its deposits with the loss of the sonic fences, that Munich and the rest of New Eden was overrun by Tiberium and classified as a Red Zone by 2054.