| 0 | - | cover | 1 | pencils: Stuart Immonen; inks: Stuart Immonen | Doctor Doom, Victor Von Doom |
| 1 | Previously In Ultimate Fantastic Four: | recap | 1 | pencils: Stuart Immonen; inks: Wade von Grawbadger; colors: Dave Stewart | Doctor Doom |
| 2 | Doom: Part 6 | comic story | 22 | script: Warren Ellis; pencils: Stuart Immonen; inks: Wade von Grawbadger; colors: Dave Stewart; letters: Chris Eliopoulos | Doctor Doom; Fantastic Four [Mister Fantastic; Human Torch [Johnny Storm]; The Thing; Invisible Girl] |
| 3 | Spider-Man & Wolverine | cover reprint (on interior page) | 1 | pencils: Matt Wagner; inks: Matt Wagner; colors: Matt Wagner | Spider-Man [Peter Parker]; Wolverine [Logan] |
| 4 | Introduction | recap | 1 | letters: typeset | Spider-Man; Wolverine |
| 5 | Spider-Man & Wolverine | comic story | 9 | script: Brian Michael Bendis; pencils: Matt Wagner; inks: Matt Wagner; colors: Jung Choi; letters: Comicraft | Spider-Man [Peter Parker]; Wolverine [Logan]; Sabretooth |
| 6 | - | in-house column | 1 | script: Joe Quesada | Joe Quesada (illo); Spider-Man (illo) |
| 7 | - | cover reprint (on interior page) | 2 | pencils: Stuart Immonen; inks: Stuart Immonen | Doctor Doom |
| 8 | Marvel Flip Magazine Checklist | promo (ad from the publisher) | 1 | letters: typeset | |
| 9 | Previously... | recap | 1 | letters: typeset | X-Men [Professor X; Cyclops; Marvel Girl; Storm; Beast; Colossus; Wolverine [Logan]; Iceman]; Dr. Cornelius; Colonel Nick Fury; Colonel John Wraith; Sabretooth; Nightcrawler; Juggernaut; Rogue; General "Thunderbolt" Ross |
| 10 | Return To Weapon X Part Six of Six | comic story | 23 | script: Mark Millar; pencils: Adam Kubert, Tom Derenick; inks: Danny Miki, Scott Hanna, Lary Stucker; colors: Richard Isanove; letters: Richard Starkings, Comicraft, Wes Abbott | X-Men [Wolverine [Logan]; Iceman; Colossus; Cyclops; Storm; Professor X; Beast; Marvel Girl]; Brotherhood of Mutants [Scarlet Witch; Quicksilver; Blob; Toad]; Nightcrawler; Colonel John Wraith; Dr. Cornelius; Juggernaut; Rogue; Colonel Nick Fury; Sabretooth |
| 11 | - | cover | 1 | pencils: Adam Kubert; colors: Richard Isanove | Professor X, Charles Xavier |