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So more lists comparing TPB and single issues, this time post No Man's Land, which ended in February 2000 with some aftermath stretching into March. After that it's "New Gotham", indicated as such also in some TPB collections. My sources are the same as in the last post. Also I rarely list the second stories in comics that contain two.
post No Man's Land
AFAIK these stories are not in in a TPB:
"The Honored Dead" -- Detective Comics #742 (March 2000)
"Constants" -- Gotham Knights #1 (March 2000)
"O'er the Land of the Free" -- Batman #575 (March 2000)
Batman: Evolution
There is an Evolution TPB reprinting Detective Comics #743-750
In single issues those were:
Evolution #1: "Whispers in the Dark" -- Detective Comics #743 (April 2000)
Evolution #2: "Unity of Purpose" -- Detective Comics #744 (May 2000)
Evolution #3: "Law of the Land" -- Detective Comics #745 (June 2000)
Evolution #4: "Aftertaste" -- Detective Comics #746 (July 2000)
"Happy Birthday Two You..." -- Detective Comics #747 (August 2000)
Urban Renewal #1 -- Detective Comics #748 (September 2000)
Urban Renewal #2 -- Detective Comics #749 (October 2000)
"Dependence" -- Detective Comics #750 (November 2000)
After that and outside of Detective Comics the following stories (featuring Batman and not part of Legends of the Dark Knight, which seems to have turned into a series with less overlap with the rest of the continuity in post No Man's Land times) were published from April 2000 to March 2001 (when the next TPB I know of is set), all not in TBP afaik:
Batman:
"In the Dark Places" -- Batman #576 (April 2000)
"Mike and Allie"-- Batman #577 (May 2000)
"He Who Lurks" -- Batman #578 (June 2000)
Orca #1: "A Matter of Principle" -- Batman #579 (July 2000)
Orca #2: "Going Under" -- Batman #580 (August 2000)
Orca #3: "Diver Down" -- Batman #581 (September 2000)
Fearless #1 -- Batman #582 (October 2000)
Fearless #2 -- Batman #583 (November 2000)
"The Dark Knight Project" -- Batman #584 (December 2000)
"Measure for Measure" -- Batman #585 (January 2001)
"Penguin Dreams" -- Batman #586 (February 2001)
Detective Comics:
A Walk in the Park #1 -- Detective Comics #751 (December 2000)
A Walk in the Park #2 -- Detective Comics #752 (January 2001)
"The Janus Double-Down" -- Detective Comics #753 (February 2001)
The Jacobian #1: "Bassinet of Death" -- Detective Comics #746/2 (July 2000)
The Jacobian #2: "The Silken Sniper" -- Detective Comics #747/2 (August 2000)
The Jacobian #3: "Desert Ninja" -- Detective Comics #748/2 (September 2000)
The Jacobian #4: "Winds of Fortune" -- Detective Comics #749/2 (October 2000)
The Jacobian #5: "The Moment's Gone" -- Detective Comics #750/2 (November 2000)
The Jacobian #6: "?" -- Detective Comics #751/2 (December 2000)
The Jacobian #7: "?" -- Detective Comics #752/2 (January 2001)
The Jacobian #8: "Dead in the Water" -- Detective Comics #753/2 (February 2001)
The Jacobian #9: "Tsunami of Fire" -- Detective Comics #754/2 (March 2001)
The Jacobian #10: "Castle in the Sky" -- Detective Comics #755/2 (April 2001)
The Jacobian #11: "The Garden of Knowledge" -- Detective Comics #756/2 (May 2001)
The Jacobian #12: "The Snake and the Detective" -- Detective Comics #757/2 (June 2001)
(The Jacobian is the second story printed in the Detective Comics issues, I'm not sure how it relates to the continuity.)
Gotham Knights:
"Down With The Ship" -- Gotham Knights #2 (April 2000)
Samsara #1: "Bad Karma" -- Gotham Knights #3 (May 2000)
Samsara #2: "Letting Go" -- Gotham Knights #4 (June 2000)
"Locked" -- Gotham Knights #5 (July 2000)
"Personal Effects" -- Gotham Knights #6 (August 2000)
"Oblation" -- Gotham Knights #7 (September 2000)
Transference #1 -- Gotham Knights #8 (October 2000)
Transference #2 -- Gotham Knights #9 (November 2000)
Transference #3 -- Gotham Knights #10 (December 2000)
Transference #4 -- Gotham Knights #11 (January 2001)
"Damages" -- Gotham Knights #12 (February 2001)
Batman: Officer Down
Officer Down is available as TPB, this crossover was originally published in March 2001. According to the info I've found the TPB doesn't contain Batgirl #12 and is thus incomplete compared to the single issues version, which was:
Officer Down #1: "These Are Your Rights" -- Batman #587 (March 2001)
Officer Down #2: "Mute Witness" -- Batgirl #12 (March 2001)
Officer Down #3: "Behind the Lines" -- Robin Vol. 2 #86 (March 2001)
Officer Down #4: "Armed and Dangerous" Birds of Prey #27 (March 2001)
Officer Down #5: "Smoking Gun" Catwoman Vol. 2 #90 (March 2001)
Officer Down #6: "Inculpatory" -- Nightwing #53 (March 2001)
Officer Down #7: "Monster in a Box" -- "Detective Comics #754 (March 2001)
Officer Down #8: "The End" -- Gotham Knights #13 (March 2001)
After that and before Bruce Wayne Murderer? the following stories where published:
Batman:
Close Before Striking #1 -- Batman #588 (April 2001)
Close Before Striking #2 -- Batman #589 (May 2001)
Close Before Striking #3 -- Batman #590 (June 2001)
Shot Through the Heart #1 -- Batman #591 (July 2001)
Shot Through the Heart #2 -- Batman #592 (August 2001)
Sanctuary #1 -- Batman #593 (September 2001)
Sanctuary #2 -- Batman #594 (October 2001)
"Out of the Past" -- Batman #595 (November 2001)
"City on Fire" -- Batman #596 (December 2001)
"Crooked Miles" -- Batman #597 (January 2002)
"Santa Klaus is Coming To Town" -- Batman #598 (February 2002)
Detective Comics:
"Here's Your Hat, What's Your Hurry?" -- Detective Comics #755 (April 2001)
"Lord of the Ring" -- Detective Comics #756 (May 2001)
"Air Time" -- Detective Comics #757 (June 2001)
Unknowing #1 -- Detective Comics #758 (July 2001)
Unknowing #2 -- Detective Comics #759 (August 2001)
Unknowing #3 -- Detective Comics #760 (September 2001)
"In Thirty Days" -- Detective Comics #761 (October 2001)
"Passings" -- Detective Comics #762 (November 2001)
"La Cucilla" -- Detective Comics #763 (December 2001)
"Hearts" -- Detective Comics #764 (January 2002)
"Vacancies" -- Detective Comics #765 (February 2002)
Gotham Knights:
"Sibling Rivalry" -- Gotham Knights #14 (April 2001)
"Far From the Tree" -- Gotham Knights #15 (May 2001)
Matatoa #1 -- Gotham Knights #16 (June 2001)
Matatoa #2 -- Gotham Knights #17 (July 2001)
"Cavernous" Gotham Knights #18 (August 2001)
"The Factor of Fear" Gotham Knights #19 (September 2001)
Retribution #1: "Sons and Lovers" -- Gotham Knights #20 (October 2001)
Retribution #2: "Contested" -- Gotham Knights #21 (November 2001)
"Bugged Out" -- Gotham Knights #22 (December 2001)
"Fear of Success" -- Gotham Knights #23 (January 2002)
"The Devil You Know" -- Gotham Knights #24 (February 2002)
Batman: Bruce Wayne Murderer? and Batman: Bruce Wayne Fugitive
That story is available as TPB.
The Batman: Bruce Wayne Murderer? TPB reprints:
Batman: 10-Cent Adventure
Batgirl #24
Batman #599-600
Birds of Prey #39-40
Detective Comics #766-767
Gotham Knights #25-26
Nightwing #65-66
Robin #98-99
The TPB prints all relevant issues, but according to this site not all pages of every issue. Also with Batman #600 it prints the first issue of what is counted already as part of Fugitive in the single issues.
The Batman: Bruce Wayne Fugitive TPB edition is split into two volumes
Batman: Bruce Wayne Fugitive Vol. 1 reprints:
Batman #601, #603
Batgirl #27, #29
Birds of Prey #41, #43
Gotham Knights #27-28
Nightwing #68-69
(again, not all pages of all issues, especially most of #601 is missing since that's a two-parter)
Batman: Bruce Wayne Fugitive Vol. 2 reprints:
Batman #605
Detective Comics #768-772
Gotham Knights #31
Those TPB omit Fugitive #14 and #15
Bruce Wayne Murderer? (in the single issues) proceeds with the following chapters:
"The Fool's Errand" -- Batman: The 10 Cent Adventure #1 (March 2002)
Bruce Wayne: Murderer? #1: "Procedure" -- Detective Comics #766 (March 2002)
Bruce Wayne: Murderer? #2: "?" -- Batgirl #24 (March 2002)
Bruce Wayne: Murderer? #3: "Bustout" -- Nightwing #65 (March 2002)
Bruce Wayne: Murderer? #4: "No Exit" -- Gotham Knights #25 (March 2002)
Bruce Wayne: Murderer? #5: "The Gun" -- Birds of Prey #39 (March 2002)
Bruce Wayne: Murderer? #6: "The Thin Line" -- Robin Vol. 2 #98 (March 2002)
Bruce Wayne: Murderer? #7: "From the Inside Out" -- Batman #599 (March 2002)
Bruce Wayne: Murderer? #8: "Timeless" -- Detective Comics #767 (April 2002)
Bruce Wayne: Murderer? #9: "The Unusual Suspects" -- Nightwing #66 (April 2002)
Bruce Wayne: Murderer? #10: "Innocent Until" -- Gotham Knights #26 (April 2002)
Bruce Wayne: Murderer? #11: "Where the Road Ends" -- Robin Vol. 2 #99 (April 2002)
Bruce Wayne: Murderer? #12: "Switchback" -- Birds of Prey #40 (April 2002)
Bruce Wayne Fugitive (in the single issues) proceeds with the following chapters:
Bruce Wayne: Fugitive #1: "The Scene of the Crime" -- Batman #600 (April 2002)
Bruce Wayne: Fugitive #2: "Felony Matters" -- Birds of Prey #41 (May 2002)
Bruce Wayne: Fugitive #3: "Turning the Town Red Part One" -- Batman #601 (May 2002)
["Turning the Town Red Part Two" -- Batman #602 (June 2002) is not labeled as part of Fugitive]
["Purity, Part 1" -- Detective Comics #768 (May 2002) is not labeled as part of Fugitive]
Bruce Wayne: Fugitive #4: "Purity, Part 2" -- Detective Comics #769 (June 2002)
Bruce Wayne: Fugitive #5: -- Batgirl #27 (June 2002)
Bruce Wayne: Fugitive #6: "Time & Motion" -- Nightwing #68 (June 2002)
Bruce Wayne: Fugitive #7: "The Mortician: Anti-Hero" -- Gotham Knights #28 (June 2002)
Bruce Wayne: Fugitive #8: "Purity, Part 3" -- Detective Comics #770 (July 2002)
Bruce Wayne: Fugitive #9: "Ins & Outs" -- Nightwing #69 (July 2002)
Bruce Wayne: Fugitive #10: "Blind Spot" -- Birds of Prey #43 (July 2002)
Bruce Wayne: Fugitive #11: "The Turning Point" -- Batman #603 (July 2002)
Bruce Wayne: Fugitive #12: "Access" -- Detective Comics #771 (August 2002)
Bruce Wayne: Fugitive #13: -- Batgirl #29 (August 2002)
Bruce Wayne: Fugitive #14: "Turnabout Part One" -- Gotham Knights #30 (August 2002)
Bruce Wayne: Fugitive #15: "Turnabout Part Two" -- Azrael: Agent of the Bat #91 (August 2002)
Bruce Wayne: Fugitive #16: "Principle" -- Detective Comics #772 (September 2002)
Bruce Wayne: Fugitive #17: "Clean" -- Batman: Gotham Knights #31 (September 2002)
Bruce Wayne: Fugitive #18: "Courage" -- Batman #605 (September 2002)
In between the Murderer and Fugitive arcs are (among others) also set:
"Murderer? Positive I.D." -- Gotham Knights #27 (May 2002)
"Madhouse!" -- Nightwing #67 (May 2002)
"The Mortician: Zombie Zero" -- Gotham Knights #29 (July 2002)
"Reasons" -- Batman #604 (August 2002)