In Red Alert 1 and its expansion packs, the Soviet Union rushed their forces through Germany (Red Alert) but this invasion took place through the east to capture Berlin as one of the Allied Nations' major Command Centers, while the west held out to the Allies next door.
During the Allied campaign and briefing of Tanya's Tale, Berlin was saved under control of the Allies. Von Esling, the Supreme Allied Commander was happy to have his city and the whole of Germany liberated. Stavros was excited about that and he was still poorly affected by Stalin's invasion of Greece. When Tanya Adams got captured, he sent Field Commander A9 to his homeland and rescue her from Soviet torture.
In Command & Conquer: Red Alert 2 and the expansion pack, Berlin still became an Allied Command Center which the German Chancellor joined Allied leaders to take out Nuclear Missile Silo (Red Alert 2) launchers, two of them in Poland by the Soviet Union. At the Reichstag, the German Chancellor contacted President Dugan to bring Albert Einstein from Berlin and help out in the clearing of Soviet forces during Operation: Liberty.
The German capital was also mentioned by the Allied Supreme Commander, General Carville of the USA who said that he is planning an invasion of the Soviet Union, before his death. The Allied Commander was sent to this city and the Chancellor sent him to Egypt, against Yuri admitting the rescue of Einstein.
In Command & Conquer: Red Alert 3, Berlin is still the Allied Command Center which Allied leaders would plan any targets on the Soviet Union if it's all clear for them. After The Famous Liberation, all of Berlin had been saved and Western Europe in Allied control.
During The Great Bear Trap, Gregor defected to this city about the Time Machine and missile sites in Soviet avenge to attack US cities in Cuba (Red Alert). The plans were given to Bingham and sends an Allied Commander (Red Alert 3) to the Caribbean with Giles, as his partner. In the Imperial story, both Bingham and Gregor went to Amsterdam, in the plans of Ackerman as a cyborg and Time Travel, which fails to prevent the rise of the Empire.