| 0 | - | cover | 1 | pencils: Frank Quitely; inks: Tim Townsend; colors: Brian Haberlin | X-Men [Cyclops; Jean Grey; Wolverine; Beast; White Queen; Professor X] |
| 1 | - | credits, title page | 3 | pencils: Frank Quitely | |
| 2 | Introduction | foreword, introduction, preface, afterword | 1 | script: Bruce Timm; letters: Bruce Timm | |
| 3 | Issue 114 | cover reprint (on interior page) | 1 | pencils: Frank Quitely; inks: Tim Townsend; colors: Brian Haberlin | X-Men [Cyclops; Jean Grey; Wolverine; Beast; White Queen; Professor X] |
| 4 | Variant Cover | cover reprint (on interior page) | 1 | pencils: Frank Quitely; inks: Tim Townsend | |
| 5 | E is for Extinction: one of three | comic story | 23 | script: Grant Morrison; pencils: Frank Quitely; inks: Tim Townsend; colors: Brian Haberlin; letters: Comicraft, Saida Temofonte | X-Men [Cyclops; Jean Grey; Wolverine; Beast; Professor X]; Cassandra Nova; Ugly John; Donald Trask; Master Mold |
| 6 | - | illustration | 1 | pencils: Frank Quitely | Cyclops |
| 7 | Issue 115 | cover reprint (on interior page) | 1 | pencils: Frank Quitely; inks: Tim Townsend; colors: Dan Kemp | Wolverine |
| 8 | Variant Cover | cover reprint (on interior page) | 1 | pencils: Barry Windsor-Smith; inks: Barry Windsor-Smith | Cyclops [Scott Summers] |
| 9 | E Is for Extinction: Two of Three | comic story | 23 | script: Grant Morrison; pencils: Frank Quitely; inks: Tim Townsend, Mark Morales; colors: HiFi Design; letters: Comicraft, Saida Temofonte, RS | X-Men [Cyclops [Scott Summers]; Jean Grey; Wolverine [Logan]; Beast [Hank McCoy]; Emma Frost [White Queen]; Professor X [Charles Xavier]]; Cassandra Nova; Ugly John; Donald Trask; Master Mold; Magneto (cameo); Negasonic Teenage Warhead (first appearance) |
| 10 | Issue 116 | cover reprint (on interior page) | 1 | pencils: Frank Quitely; inks: Tim Townsend; colors: HiFi Design | Emma Frost [White Queen] |
| 11 | E is for Extinction: Three of Three | comic story | 23 | script: Grant Morrison; pencils: Frank Quitely; inks: Mark Morales, Dan Green; colors: HiFi Design; letters: Richard Starkings, Comicraft, Saida Temofonte | X-Men [Cyclops; Jean Grey; Wolverine; Beast; Emma Frost [White Queen]; Professor X]; Cassandra Nova |
| 12 | 2001 Annual | cover reprint (on interior page) | 1 | pencils: Leinil Francis Yu; inks: Leinil Francis Yu; colors: Leinil Francis Yu | X-Men [Wolverine; Cyclops; White Queen] |
| 13 | The Man from Room X | comic story | 41 | script: Grant Morrison; pencils: Leinil Francis Yu; inks: Gerry Alanguilan; colors: HiFi Design; letters: RS, Comicraft, Saida | X-Men [Beast [Henry McCoy]; Cyclops [Scott Summers]; Jean Grey; White Queen [Emma Frost]; Wolverine [Logan; James Howlett]]; Domino [Beatrice]; Xorn [Kuan-Yin] (first appearance); Mr. Ao Jun (villain, dies); John Sublime (villain); U-Men [Jan; Biro; Harriet] (villains) |
| 14 | Issue 117 | cover reprint (on interior page) | 1 | pencils: Frank Quitely; inks: Tim Townsend; colors: Hi-Fi Design | Beast |
| 15 | Danger Rooms | comic story | 23 | script: Grant Morrison; pencils: Ethan Van Sciver; inks: Prentis Rollins; colors: HiFi Design; letters: RS, Comicraft, Saida Temofonte | X-Men [Cyclops; Jean Grey; Wolverine; Beast; Emma Frost [White Queen]; Professor X]; Cassandra Nova; Beak [Barnell Bohusk]; Gladiator (cameo); Smasher (cameo); Lilandra (cameo) |
| 16 | Issue 118 | cover reprint (on interior page) | 1 | pencils: Frank Quitely; inks: Tim Townsend; colors: HiFi Design | Cyclops |
| 17 | Germ Free Generation: one of three | comic story | 23 | script: Grant Morrison; pencils: Ethan Van Sciver; inks: Scott Hanna, Sandu Florea, Prentis Rollins; colors: HiFi Design; letters: Comicraft | X-Men [Cyclops; Jean Grey; Wolverine; Beast; Emma Frost [White Queen]; Professor X]; Cassandra Nova; John Sublime; Angel [Angel Salvadore] (introduction) |
| 18 | Issue 119 | cover reprint (on interior page) | 1 | pencils: Frank Quitely; inks: Tim Townsend; colors: HiFi Design | Angel [Angel Salvadore] |
| 19 | Germ Free Generation: two of three | comic story | 23 | script: Grant Morrison; pencils: Igor Kordey; inks: Igor Kordey; colors: HiFi Design; letters: RS, Comicraft, Saida Temofonte | X-Men [Cyclops; Jean Grey; Wolverine; Beast; Emma Frost [White Queen]]; John Sublime; Angel [Angel Salvadore]; Beak; Stepford Cuckoos [Celeste; Esme; Irma; Phoebe; Sophie] (cameo) |
| 20 | Issue 120 | cover reprint (on interior page) | 1 | pencils: Frank Quitely; inks: Tim Townsend; colors: HiFi Design | Jean Grey |
| 21 | Germ Free Generation: three of three | comic story | 23 | script: Grant Morrison; pencils: Igor Kordey; inks: Igor Kordey; colors: HiFi Design; letters: Richard Starkings, Comicraft, Saida Temofonte | X-Men [Cyclops; Jean Grey; Wolverine; Beast; Emma Frost [White Queen]]; John Sublime; Angel [Angel Salvadore]; Cassandra Nova; Stepford Cuckoos [Celeste; Esme; Irma; Phoebe; Sophie]; Irina Clayton |
| 22 | Issue 121 | cover reprint (on interior page) | 1 | pencils: Frank Quitely; inks: Frank Quitely; colors: HiFi Design | Professor X; Cassandra Nova |
| 23 | Silence: Psychic Rescue In Progress | comic story | 23 | script: Grant Morrison; pencils: Frank Quitely; inks: Frank Quitely; colors: HiFi Design; letters: Richard Starkings | X-Men [Cyclops; Jean Grey; Wolverine; Emma Frost [White Queen]; Professor X]; Cassandra Nova |
| 24 | Issue 122 | cover reprint (on interior page) | 1 | pencils: Frank Quitely; inks: Tim Townsend; colors: HiFi Design | Lilandra |
| 25 | Imperial | comic story | 23 | script: Grant Morrison; pencils: Frank Quitely; inks: Tim Townsend, Rich Perrotta, Sandu Florea; colors: HiFi Design; letters: RS, Comicraft, Saida Temofonte | X-Men [Cyclops; Jean Grey; Wolverine; Emma Frost [White Queen]; Beast; Professor X]; Cassandra Nova; Lilandra; Smasher; Immundra; Xorn; Rinpoche; Angel [Angel Salvadore] (cameo); Stepford Cuckoos (cameo); Irina Clayton (cameo) |
| 26 | Issue 123 | cover reprint (on interior page) | 1 | pencils: Tony Harris; inks: Ray Snyder; colors: J. D. Mettler | Wolverine |
| 27 | Testament | comic story | 23 | script: Grant Morrison; pencils: Ethan Van Sciver, Tom Derenick; inks: Tim Townsend, Danny Miki, Scott Hanna, Sandu Florea; colors: HiFi Design; letters: Richard Starkings, Comicraft, Saida Temofonte | Cyclops; Jean Grey; Wolverine; White Queen [Emma Frost]; Angel [Angel Salvadore]; Beast; Stepford Cuckoos [Celeste; Esme; Irma; Phoebe; Sophie]; Cassandra Nova; Professor X; Xorn; Superguardian Team [Gladiator; Arc; Stuff] |
| 28 | Issue 124 | cover reprint (on interior page) | 1 | pencils: Frank Quitely; inks: Tim Townsend; colors: HiFi Design | Xorn |
| 29 | Superdestroyer | comic story | 23 | script: Grant Morrison; pencils: Igor Kordey; inks: Igor Kordey; colors: HiFi Design; letters: Comicraft | Cyclops; Jean Grey; Wolverine; White Queen [Emma Frost]; Angel [Angel Salvadore]; Beast; Stepford Cuckoos Stepford Cuckoos [Celeste; Esme; Irma; Phoebe; Sophie]; Cassandra Nova; Professor X; Xorn; Lilandra; Superguardian Team [Gladiator; Stuff; G-Type; Araki; Neosaurus; Plutonia; Oracle; Manta; Fade |
| 30 | Issue 125 | cover reprint (on interior page) | 1 | pencils: Ethan Van Sciver | Beak |
| 31 | Losers | comic story | 22 | script: Grant Morrison; pencils: Igor Kordey; inks: Igor Kordey; colors: HiFi Design; letters: RS, Comicraft, Saida Temofonte; editing: Mark Powers | Lilandra; Cassandra Nova; Charles Xavier; Araki; G-Type; Cyclops; Xorn; Angel [Angel Salvadore]; Stepford Cuckoos [Celeste; Esme; Irma; Phoebe; Sophie]; Beak; White Queen; Jean Grey; Beast; Wolverine; Stuff; Gladiator; Manta; Plutonia; Smasher; Trish Tilby |
| 32 | - | illustration | 1 | | Xorn |
| 33 | Issue 126 | cover reprint (on interior page) | 1 | pencils: Frank Quitely; inks: Tim Townsend | Professor X [Charles Xavier]; Cyclops; Wolverine; White Queen; Jean Grey; Beast; Angel [Angel Salvadore]; Stepford Cuckoos [Celeste; Esme; Irma; Phoebe; Sophie]; Beak; Glob Herman; Redneck; Dummy; Tattoo; Radian; Ernst; Quentin Quire |
| 34 | All Hell | comic story | 32 | script: Grant Morrison; pencils: Frank Quitely; inks: Tim Townsend; colors: Brian Haberlin; letters: Richard Starkings, Comicraft, Saida Temofonte; editing: Mark Powers, Mike Marts | Cyclops; Xorn; Charles Xavier; Lilandra; Cassandra Nova; Araki; Manta; Plutonia; Smasher; Gladiator; Beak; Angel [Angel Salvadore]; Stepford Cuckoos [Celeste; Esme; Irma; Phoebe; Sophie]; Stuff; White Queen [Emma Frost]; Jean Grey; Beast; Wolverine |
| 35 | Morrison Manifesto | text article | 11 | script: Grant Morrison, Mark Powers; pencils: Frank Quitely; inks: Frank Quitely; colors: Frank Quitely; letters: Mark Powers | |
| 36 | Frank Quitely Character Sketches | illustration | 1 | script: Frank Quitely; pencils: Frank Quitely; inks: Frank Quitely; colors: Frank Quitely; letters: Frank Quitely | |
| 37 | Igor Kordey | illustration | 1 | pencils: Igor Kordey | |
| 38 | Ethan Van Sciver | illustration | 1 | pencils: Ethan Van Sciver; inks: Ethan Van Sciver | |