- X-Men vs. Apocalypse, vol.1: The Twelve
- Reprints Uncanny X-Men #376-377 (January 2000 – February 2000); Cable #73-76 (November 1999 – February 2000); X-Men #96-97 (January 2000 – February 2000); & Wolverine #145-147 (December 1999 – February 2000).
- X-Men Vs. Apocalypse, vol.2: Ages of Apocalypse
- Reprints X-51 #8 (March 2000); Uncanny X-Men #378 (March 2000) & Annual 1999; Cable #77 (March 2000); Wolverine #148 (March 2000); X-Men Unlimited #26 (March 2000); X-Men #98 (March 2000); & X-Men: The Search for Cyclops #1-4 (October 2000 – March 2001).
- Daredevil, vol.2: Parts of a Hole
- Reprints Daredevil #9–15 (December 1999 – April 2001).
- Captain America by Dan Jurgens, vol.1
- Reprints Captain America #25-34 (January 2000 – October 2000).
- The Punisher: Welcome Back, Frank
- Reprints The Punisher #1-12 (April 2000 – March 2001 ).
- Cable: Revolution
- Reprints Cable #79-96 (May 2000 – October 2001).
- Avengers Assemble, vol.3
- Reprints Avengers #24-34 (January 2000 – November 2000) & Annual (2000); & Thunderbolts #42-44 (September 2000 – November 2000).
This book immediately follows the Eighth Day crossover. - Avengers Infinity Classic
- Reprints Avengers Infinity #1-4 (September 2000 – December 2000).
Immediately precedes Maximum Security. - Avengers / X-Men: Maximum Security
- Reprints Avengers #35 (December 2000); Bishop: The Last X-Man #15 (December 2000); Captain America #36 (December 2000); Gambit #23 (December 2000); Iron Man #34-35 (November 2000 – December 2000); Maximum Security #1-3 (November 2000 – January 2001); Maximum Security: Dangerous Planet #1 (October 2000); Thor #30 (December 2000); Uncanny X-Men #387 (December 2000); X-Men #107 (December 2000); & X-Men Unlimited #29 (December 2000).
For a more detailed reading order for this story, go here. - Avengers Assemble, vol.4
- Reprints Avengers #35-44 (December 2000 – September 2001) & Annual 2001 (September 2001); Maximum Security #1-3 (November 2000 – January 2001) & Maximum Security: Dangerous Planet #1 (October 2000).
- Black Panther by Christopher Priest: The Complete Collection, vol.2
- Reprints Black Panther #18–35 (May 2000 – October 2001) & Deadpool #44 (September 2000).
- Deadpool Classic, vol.6
- Reprints Deadpool #34-45 (November 1999 – October 2000) & Black Panther #23 (October 2000).
- Daredevil: Ninja
- Reprints Daredevil: Ninja #1-3 (December 2000 – May 2001).
- X-Men: Dream’s End
- Reprints Uncanny X-Men #388-390 (January 2001 – March 2001); Cable #87 (January 2001); Bishop: The Last X-Men #16 (January 2001); & X-Men #108-110 (January 2001 – March 2001).
- Daredevil, vol.3: Wake Up
- Reprints Daredevil #16-19 (May 2001 – August 2001).
- Fantastic Four: Resurrection of Galactus
- Reprints Fantastic Four #46-50 (October 2001 – February 2002) & Annual (2001).
- Avengers Assemble, vol. 5
- Reprints Avengers #41-56 (June 2001 – September 2002) & Annual 2001.
Avengers: ‘Nuff Said- Reprints Avengers #49 (February 2002); Black Panther #39 (February 2002); Captain America #50 (February 2002); Iron Man #49 (February 2002); & Thor #44 (February 2002).
- Doom
- Reprints Doom #1-3 (October 2000 – December 2000); & Doom: The Emperor Returns #1-3 (January 2002 – March 2002).
- Fantastic Four/Inhumans
- Reprints Inhumans #1-4 (June 2000 – October 2000); & Fantastic Four #51-54 (March 2002 – June 2002).
- New X-Men, vol.1
- Reprints New X-Men #114-126 (July 2001 – July 2002) & Annual 2001.
- X-Men: X-Corps
- Reprints Uncanny X-Men #394-409 (July 2001 – September 2002) & Annual 2001.
- X-Treme X-Men, vol.4: Mekanix
- Reprints Mekanix #1-6 (December 2002 – May 2003); & X-Men Unlimited #36 (Kitty Pryde story only, July 2002).
- –> X-Treme X-Men by Claremont & Larroca: A New Beginning
- Reprints X-Treme X-Men #1-5 (January 2023 – May 2023).
- Cable: Soldier X
- Reprints Cable #97-107 (November 2001 – September 2002) & Soldier X #1-12 (September 2002 – August 2003).
- X-Men: ‘Nuff Said
- Reprints New X-Men #121 (February 2002); Uncanny X-Men #401 (February 2002); Wolverine #171 (February 2002); X-Force #123 (February 2002); & X-Treme X-Men #8 (February 2002).
- —> Fantastic Four: Antithesis
- Reprints Fantastic Four: Antithesis #1-4 (October 2020 – January 2021); Fantastic Four #60 (October 2002); & X-Men #65 (February 1970).
- Spider-Man: The Lifeline Tablet Saga
- Reprints Amazing Spider-Man #68-75 (January 1969 – August 1969); & Spider-Man: Lifeline #1-3 (April 2001 – June 2001).
The second part of this story takes place at this time, the first part much earlier. - Captain America: Marvel Knights, vol.1
- Reprints Captain America #1-16 (June 2002 – October 2003).
- Alias, vol.1
- Reprints Alias #1-9 (November 2001 – July 2002).
- –> Daredevil: Father
- Reprints Daredevil: Father #1-6 (June 2004 – February 2007).
Must occur before the revelation of Daredevil’s secret identity in Daredevil: Out - Deadline
- Reprints Deadline #1-4 (June 2002 – September 2002).
Must occur before the revelation of Daredevil’s secret identity in Daredevil: Out - Daredevil, vol.4: Underboss
Reprints Daredevil #26-31 (December 2001 – May 2002).- Peter Parker, Spider-Man: Return of the Green Goblin
- Reprints Peter Parker: Spider-Man #44-47 (August 2002 – October 2002).
- Daredevil, vol.5: Out
- Reprints Daredevil #32-37 (June 2002 – November 2002).
- New X-Men, vol.2
- Reprints New X-Men #127-141 (August 2002 – July 2003).
- Alias, vol.2: Come Home
- Reprints Alias #11-15 (September 2002 – December 2002).
This volume parallels the events of Daredevil: Out. - JLA/Avengers
- Reprints JLA/Avengers #1-4 (September 2003 – February 2004).
Crosses over with the Post-Crisis DC Universe. - Avengers: The Complete Collection by Geoff Johns, vol.1
- Reprints Avengers #57-63 (October 2002 – March 2003); Avengers Icons: The Vision #1-4 (October 2002 – January 2003); Iron Man #64 (March 2003); & Thor #58 (March 2003).
Includes all three parts of the Standoff storyline. - Thor: Gods on Earth
- Reprints Thor #51-58 (September 2002 – March 2003); Avengers #63 (March 2003); & Iron Man #64 (March 2003).
Includes all three parts of the Standoff storyline. - Fantastic Four, vol.2: Unthinkable
- Reprints Fantastic Four #67-70 (May 2003 – August 2003); & #500-502 (September 2003 – November 2003).
- Silver Surfer: Communion
- Reprints Silver Surfer #1-6 (September 2003 – April 2004).
- Young Inhumans
- Reprints Inhumans #1-12 (June 2003 – June 2004).
- Daredevil, vol.6: Lowlife
- Reprints Daredevil #41-45 (March 2003 – May 2003).
- Alias, vol.3: The Underneath
- Reprints Alias #10 & 16-21 (August 2002 & January 2003 – June 2003).
This volume parallels the events of Daredevil: Lowlife. - Daredevil, vol.7: Hardcore
- Reprints Daredevil #46-50 (June 2003 – October 2003).
- Runaways, vol.1: Pride & Joy
- Reprints Runaways #1-6 (July 2003 – November 2003).
- The Avengers: The Complete Collection by Geoff Johns, vol.2
- Reprints Avengers #64-76 (April 2003 – February 2004).
- Exiles Ultimate Collection, Book 2
- Reprints Exiles #20-37 (February 2003 – January 2004); & X-Men Unlimited #41 (March 2003).
Crosses over with the Age of Apocalypse. - Alias, vol.4: The Secret Origins of Jessica Jones
- Reprints Alias #22-28 (July 2003 – January 2004).
- New X-Men, vol.3
- Reprints New X-Men #142-154 (August 2003 – May 2004).
- Mystique by Brian K. Vaughan Ultimate Collection
- Reprints Mystique #1-13 (June 2003 – June 2004).
- Daredevil, vol.8: Echo – Vision Quest
- Reprints Daredevil #51-55 (November 2003 – February 2004).
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