To seal the Fuhrer's power the chief of staff of the army was eliminated in the mid to late thirties. I don't recall his name, but I think he was arrrested on bogus charges, which damaged the army's reputation, and also executed, which sent a signal to other generals. The Waffen SS, far from being a special forces unit, had complete armored divisions and was seen as a new German Army remade in the mold of the perfect Ayrian killing machine, absolutely ruthless and loyal to the regime to the end.
On the chief of staff arrested, you're probably thinking of Ludwig Beck. Beck was cleared by an honor court, IIRC. I think his successor was von Fritsch, who essentially committed suicide by exposing himself to fire during the Polish campaign, but their might have been one or two in between them. It's been 30+ years since I read Gordon Craig's Politics of the Prussian Army and a couple of other books (Wheeler Bennett comes to mind) on the German army.
It was General Kurt von Schleicher whom the Nazis murdered during the Night of Long Knives (when Hitler took out Ernst Roehm and the Sturm Abteilung (SA)).
It was von Fritsch whom the Nazis charged (falsely) with being a homosexual and retired him early. He was the one who died in Poland in 1939.