I have always been a fan of stories where the hero has failed and there is a need for redemption or the hero needs to find it within themselves to be a hero again. I love stories like Superman: Exile, Superman: Grounded, Batman: Knightfall. Is there anything that fits this strange criteria. No specific character Needed, Superman and Batman are my favorites but I love almost all of DC’s pantheon.
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I don’t care much for the story, but Superman: For Tomorrow would fit that description.
As for Batman, how about “Blind Justice” by Sam Hamm? It appears in Detective Comics #598, 599, and 600. And there’s always the Legends of the Dark Knight story Venom.
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I love For Tomorrow, so I’ll second that one. Good call, @AlexanderKnox! 
As for other Superman tales fitting your query, give Godfall a gander. It consists of:
-Action Comics (1938-2011) #812
-Adventures of Superman (1987-2006) #625
-Superman (1986-2006) #202
-Action Comics #813
-Adventures of Supreman #626
-Superman #203
Now, the bad news is that Action Comics #'s 812 and 813 are the only parts available in digital, with the others being print-only so far.
The good news is this story is from the mid-'00s, and as a result is very easy to find in single issues and/or trade (available in hardcover and softcover editions, both of which are out of print, but easy to find).
So, give Godfall a whirl. Fair warning though, prepare to be seduced by the arc’s beautiful artwork. Michael Turner covers and Talent Caldwell interiors equal a sumptuous affair.
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For Tomorrow came to my mind right away when I read the original post. Agree with @Vroom and @AlexanderKnox. One of my favorite stories.
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The recently arrived on DC Universe “Man and Superman” fits this perfectly. As does Superman for All Seasons.
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I loved Superman Grounded, it’s at my local library, and I check it out at least once a week. I can’t say that I know of any other superman comics that haven’t already been listed, sorry.
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There was a very good two-parter called Crisis at Hand in Superman: Man of Steel #16 and Superman #72 from 1992
It basically brings the Wife Beater situation from Action Comics #1 into Post Crisis continuity and illustrates how Superman can’t always fix some of the terrible things that people do to each other.
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Superman/Batman Sorcerer Kings. Superman/Batman issues #78-#84.
America VS the JSA. It’s all about a diary Batman left behind accusing JSA members of things. I’m being extremely vague cuz I don’t want to spoil it. These are 2 of my favorite reads. Both fit the criteria.
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Love both of these stories. Kingdom Come might be my absolute favorite version of Superman.
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Hmm. How about some classic “Superman has a bad day” stories from the end of the Silver Age? There’s Action Comics #358-359, where he’s framed for murder. And there’s Action Comics #368-369, where Superman discovers that all crime has stopped on Earth…and then manages to undo this utopia. Or how about that time he had amnesia in Action Comics #371, 372, 374, & 375. Man, the late 1960s were rough on the Man of Tomorrow, no?
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@AlexanderKnox: Great Silver Age choices for Supes having a bad day. I read all those wonderful stories as a kid and still enjoy them to this day. Action Comics #'s 358 & 359 feature early Neal Adams Superman covers that were so different and striking for that period. And the two-part story by Leo Dorfman is typical of his character-driven Superman tales where The Man of Steel is presented with a problem he can’t punch his way out of. It takes that incredible super-mind (something that was always on display in the Silver Age) and a little help from a “friend” to clear his name of a murder charge. Good stuff!!
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I will second Superman: Godfall. This was a great story and the artwork makes it extremely to fall in love with it.
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In general, the late '60s weren’t very super, man.
However, for comics that was a pretty groovy time, so it wasn’t all white rabbits and such. Kicks just kept getting harder to find, man. 
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