| 0 | - | cover | 1 | pencils: Brandon Peterson; inks: Brandon Peterson; colors: Brandon Peterson | Anole, Victor Borkowski, Cannonball, Gentle, Sam Guthrie, Ororo Munroe, Nightcrawler, Storm, Kurt Wagner |
| 1 | - | cover reprint (on interior page) | 1 | pencils: Brandon Peterson; inks: Brandon Peterson; colors: Brandon Peterson | Anole, Victor Borkowski, Cannonball, Gentle, Sam Guthrie, Ororo Munroe, Nightcrawler, Storm, Kurt Wagner |
| 2 | Recap | recap | 1 | letters: typeset | |
| 3 | Danger Room | comic story | 8 | script: Mike Carey; pencils: Brandon Peterson; inks: Brandon Peterson; colors: Justin Ponsor; letters: Virtual Calligraphy's Cory Petit | Cannonball, Paige Guthrie, Sam Guthrie, Husk |
| 4 | Home | comic story | 8 | script: Craig Kyle, Chris Yost; pencils: Sana Takeda; inks: Sana Takeda; colors: Sana Takeda; letters: Virtual Calligraphy's Cory Petit | Black Panther, Gentle, Ororo Munroe, Storm, T'Challa |
| 5 | Blend In | comic story | 8 | script: Skottie Young; pencils: Skottie Young; inks: Skottie Young; colors: Skottie Young, Jean-Francois Beaulieu; letters: Virtual Calligraphy's Cory Petit | Anole, Jean-Paul Beaubier, Victor Borkowski, Northstar |
| 6 | Belong | comic story | 6 | script: Chris Yost; pencils: David Lafuente; inks: David Lafuente; colors: Guru-eFX; letters: Virtual Calligraphy's Cory Petit | Erik Lehnsherr, Emma Frost, Laura Kinney, Lady Deathstrike, Magneto, Sofia Mantega, Owl, Leland Owlsley, Yuriko Oyama, Wind Dancer, X-23 |
| 7 | Migas | comic story | 8 | script: Matt Fraction; pencils: Jamie McKelvie; inks: Jamie McKelvie; colors: Guru-eFX; letters: Virtual Calligraphy's Cory Petit | Nightcrawler, Scalphunter, Kurt Wagner |
| 8 | - | cover reprint (on interior page) | 1 | pencils: Brandon Peterson; inks: Brandon Peterson; colors: Brandon Peterson | Beast, Forge, Havok, Hank McCoy, Alex Summers |
| 9 | Lights Out | comic story | 8 | script: Mike Carey; pencils: Scot Eaton; inks: Andrew Hennessy; colors: Frank D'Armata; letters: Virtual Calligraphy's Joe Caramagna | Beast, Martha Johansson, Logan, Hank McCoy, Wolverine |
| 10 | Planting Seeds | comic story | 6 | script: C. B. Cebulski; pencils: David Yardin; inks: David Yardin; colors: John Rauch; letters: Virtual Calligraphy's Joe Caramagna | Banshee, Sean Cassidy, Colossus, Cyclops, Logan, Magik, Ororo Munroe, Kitty Pryde, Piotr Rasputin, Illyana Rasputina, Storm, Scott Summers, Wolverine |
| 11 | The Hole | comic story | 8 | script: Andy Schmidt; pencils: Frazer Irving; inks: Frazer Irving; colors: Frazer Irving; letters: Virtual Calligraphy's Joe Caramagna | Bishop, Lucas Bishop, Cable, Colossus, Havok, Lady Deathstrike, Logan, Yuriko Oyama, Piotr Rasputin, Alex Summers, Vulcan, Wolverine, Professor X, Charles Xavier |
| 12 | Idee Fixe | comic story | 8 | script: Duane Swierczynski; pencils: Chris Burnham; inks: Chris Burnham; colors: Nathan Fairbairn; letters: Virtual Calligraphy's Joe Caramagna | Bishop, Lucas Bishop, Forge |
| 13 | The Sun Also Sets | comic story | 8 | script: C. B. Cebulski; pencils: David Lafuente; inks: David Lafuente; colors: Christina Strain; letters: Virtual Calligraphy's Joe Caramagna | Cannonball, Sam Guthrie, Hela, Lady Deathstrike, Wanda Maximoff, Dani Moonstar, Odin, Yuriko Oyama, Scarlet Witch, Rahne Sinclair, Wolfsbane, Professor X, Charles Xavier |
| 14 | - | cover reprint (on interior page) | 1 | pencils: Scott Kolins; inks: Scott Kolins; colors: Chris Sotomayor | Caliban, Ch'od, Corsair, Darwin, Hepzibah, Jamie Madrox, Magik, Lilandra Neramani, Phoenix, Random, Illyana Rasputina, Raza, Riptide, Christopher Summers |
| 15 | X-Men: Messiah Complex - Mutant Files Credits | credits, title page | 1 | letters: typeset | |
| 16 | Anole | character profile | 1 | script: Eric J. Moreels; pencils: Humberto Ramos | Anole, Victor Borkowski |
| 17 | Cannonball | character profile | 2 | script: Eric J. Moreels | |
| 18 | Daken | character profile | 1 | script: Mike Fichera; pencils: Steve Dillon, Joe Quesada | Akihiro, Daken |
| 19 | Darwin | character profile | 1 | script: Eric J. Moreels; pencils: Marc Silvestri, Pete Woods | Darwin |
| 20 | Dazzler | character profile | 3 | script: Sean McQuaid | Alison Blaire, Dazzler |
| 21 | Excalibur | character profile | 2 | script: Stuart Vandal; pencils: Michael Ryan | |
| 22 | Exiles | character profile | 3 | script: David Wiltfong | |
| 23 | Kimura | character profile | 1 | script: Ronald Byrd; pencils: Paco Medina | Kimura |
| 24 | Korvus | character profile | 1 | script: Chris Biggs; pencils: Billy Tan | Korvus |
| 25 | Lady Mastermind | character profile | 1 | script: Eric J. Moreels; pencils: Humberto Ramos | Lady Mastermind, Regan Wyngarde |
| 26 | Lifeguard & Slipstream | character profile | 1 | script: Eric J. Moreels; pencils: Salvador Larroca | Davis Cameron, Heather Cameron, Lifeguard, Slipstream |
| 27 | Magik | character profile | 2 | script: Stuart Vandal | Magik, Illyana Rasputina |
| 28 | Marauders | character profile | 2 | script: Eric J. Moreels | |
| 29 | Irene Merryweather | character profile | 1 | script: Eric J. Moreels; pencils: Patrick Zircher, Michael Ryan | Irene Merryweather |
| 30 | Cassandra Nova | character profile | 1 | script: Eric J. Moreels; pencils: Frank Quitely, John Cassaday | Cassandra Nova |
| 31 | Phoenix | character profile | 4 | script: Eric J. Moreels | Phoenix |
| 32 | Predator X | character profile | 1 | script: Eric J. Moreels; pencils: Marc Silvestri, Paco Medina | Predator X |
| 33 | Savage Land Mutates | character profile | 2 | script: Chad Anderson | |
| 34 | Selene | character profile | 2 | script: Chad Anderson | Selene Gallio |
| 35 | Shi'ar | character profile | 4 | script: Chad Anderson | |
| 36 | Starjammers | character profile | 3 | script: Eric J. Moreels | |
| 37 | SWORD | character profile | 1 | script: Michael Hoskin; pencils: John Cassaday; inks: John Cassaday; colors: Laura Martin | |
| 38 | Trish Tilby | character profile | 1 | script: Eric J. Moreels; pencils: Randy Green | Trish Tilby |
| 39 | X-Cell | character profile | 1 | script: Stuart Vandal; pencils: Khoi Pham | |
| 40 | X-Factor Investigations | character profile | 2 | script: Stuart Vandal; pencils: Pablo Raimondi; inks: Pablo Raimondi | |
| 41 | Armor | character profile | 0.5 | script: Eric J. Moreels; pencils: John Cassaday; inks: John Cassaday; colors: Laura Martin | Armor, Hisako Ichiki |
| 42 | Ghoul | character profile | 0.5 | script: Chris Biggs; pencils: Ramón Bachs | Ghoul |
| 43 | Johnny Dee | character profile | 0.5 | script: Chad Anderson; pencils: Yanick Paquette | Johnny Dee |
| 44 | Mammomax | character profile | 0.5 | script: Madison Carter; pencils: Randy Green | Mammomax |
| 45 | Pandemic | character profile | 0.5 | script: Eric J. Moreels; pencils: Humberto Ramos | Pandemic |
| 46 | Petra | character profile | 0.5 | script: Eric J. Moreels; pencils: David Yardin | Petra |
| 47 | Sway | character profile | 0.5 | script: Eric J. Moreels; pencils: David Yardin | Sway |
| 48 | X-Men Roster Update | character profile | 0.5 | script: Eric J. Moreels | |
| 49 | Character Sketches | illustration | 1 | pencils: David Lafuente | |
| 50 | The Sun Also Sets Pages 5 and 6 Layouts | illustration | 1 | pencils: David Lafuente | |