The more ambitious, but less successful sequel to the original Secret Wars. It fits into the main timeline here.

Secret Wars II #1 Secret Wars II Omnibus
New Mutants #30 [1] Secret Wars II Omnibus
New Mutants Omnibus, vol.2
New Mutants Epic Collection, vol.2: The Demon Bear Saga
New Mutants Classic, vol.4
Iron Man #197 Secret Wars II Omnibus
Iron Man: Iron Monger
Captain America #308 Secret Wars II Omnibus
Captain America Epic Collection, vol.12: Society of Serpents
Captain America by Mark Gruenwald Omnibus, vol.1
Uncanny X-Men #196 Secret Wars II Omnibus
Marvel Masterworks: The Uncanny X-Men. vol.12
The Uncanny X-Men Omnibus, vol.5
Secret Wars II #2 [2] Secret Wars II Omnibus
Fantastic Four Visionaries – John Byrne, vol.6
Web of Spider-Man #6 Secret Wars II Omnibus
Essential Web of Spider-Man, vol.1
Web of Spider-Man Omnibus
Amazing Spider-Man Masterworks, vol.25
Amazing Spider-Man Epic Collection, vol.15: Ghosts Of The Past
Amazing Spider-Man #268 Secret Wars II Omnibus
Amazing Spider-Man Masterworks, vol.25
Amazing Spider-Man Epic Collection, vol.15: Ghosts Of The Past
Essential Web of Spider-Man, vol.1
Web of Spider-Man Omnibus
Fantastic Four #282 Secret Wars II Omnibus
Fantastic Four Visionaries – John Byrne, vol.6
Fantastic Four by John Byrne Omnibus, vol.2
Secret Wars II #3 Secret Wars II Omnibus
New Avengers: Illuminati #3 [3] New Avengers: Iluminati
New Avengers by Brian Michael Bendis: The Complete Collection, vol.3
Avengers #260 Secret Wars II Omnibus
Avengers: The Legacy of Thanos
Daredevil #223 Secret Wars II Omnibus
Fantastic Four #285 Secret Wars II Omnibus
Fantastic Four Visionaries – John Byrne, vol.7
Fantastic Four by John Byrne Omnibus, vol.2
Incredible Hulk #312 Secret Wars II Omnibus
Incredible Hulk: Crossroads
Incredible Hulk Epic Collection, vol.13: Crossroads
Secret Wars II #4 Secret Wars II Omnibus
Essential Dazzler, vol.2
Dazzler Omnibus
Dazzler #40 Secret Wars II Omnibus
Essential Dazzler, vol.2
Dazzler Omnibus
Alpha Flight #28 Secret Wars II Omnibus
Alpha Flight Classic, vol.3
Alpha Flight by John Byrne
ROM #72 [4] ROM: The Original Marvel Years Omnibus, vol.3
Avengers #261 Secret Wars II Omnibus
Avengers: The Legacy of Thanos
Secret Wars II #5 Secret Wars II Omnibus
The Thing #30 Secret Wars II Omnibus
The Thing Omnibus
Doctor Strange Vol. 2 #74 Secret Wars II Omnibus
Dr. Strange: Into the Dark Dimension
Secret Wars II #6 Secret Wars II Omnibus
Power Pack #18 Secret Wars II Omnibus
Power Pack Classic, vol.3
Power Pack Classic Omnibus
Thor #363 Secret Wars II Omnibus
Thor by Walt Simonson, vol.3
Thor by Walt Simonson Omnibus
Power Pack Classic, vol.3
Power Pack Classic Omnibus
Cloak and Dagger Vol. 2 #4 Secret Wars II Omnibus
Cloak & Dagger: Lost and Found
Cloak and Dagger Omnibus, vol.1
Micronauts #16 [4] Micronauts: The Original Marvel Years Omnibus, vol.3
Power Man and Iron Fist #121 Secret Wars II Omnibus
Power Man and Iron Fist Epic Collection, vol.4: Hardball
Secret Wars II #7 Secret Wars II Omnibus
Defenders #152 Secret Wars II Omnibus
Defenders Epic Collection, vol.9: The End of All Songs
New Mutants #36 Secret Wars II Omnibus
New Mutants Omnibus, vol.2
New Mutants Epic Collection, vol.3: Asgardian Wars
New Mutants Classic, vol.5
Amazing Spider-Man #273 Secret Wars II Omnibus
Amazing Spider-Man Masterworks, vol.26
Peter Parker, the Spectacular Spider-Man #111 Secret Wars II Omnibus
Essential Peter Parker, the Spectacular Spider-Man, vol.5
Uncanny X-Men #202 Secret Wars II Omnibus
Marvel Masterworks: The Uncanny X-Men, vol.13
The Uncanny X-Men Omnibus, vol.5
X-Men Mutant Massacre Prologue Omnibus
X-Men: Ghosts
Secret Wars II #8 Secret Wars II Omnibus
New Mutants #37 [5] Secret Wars II Omnibus
New Mutants Omnibus, vol.2
New Mutants Epic Collection, vol.3: Asgardian Wars
New Mutants Classic, vol.5
Amazing Spider-Man #274 [5] Secret Wars II Omnibus
Amazing Spider-Man Masterworks, vol.26
Avengers #265 Secret Wars II Omnibus
Avengers: The Once and Future Kang
Avengers Epic Collection, vol.16: Under Siege
Fantastic Four #288 Secret Wars II Omnibus
Fantastic Four Visionaries – John Byrne, vol.8
Fantastic Four by John Byrne Omnibus, vol.2
Uncanny X-Men #203 Secret Wars II Omnibus
Marvel Masterworks: The Uncanny X-Men, vol.13
The Uncanny X-Men Omnibus, vol.5
X-Men Mutant Massacre Prologue Omnibus
X-Men: Ghosts
Secret Wars II #9 Secret Wars II Omnibus
Epilogues:
Avengers #266 Secret Wars II Omnibus
Avengers: The Once and Future Kang
Avengers Epic Collection, vol.16: Under Siege
New Mutants #38 [6] New Mutants Omnibus, vol.2
New Mutants Epic Collection, vol.3: Asgardian Wars
New Mutants Classic, vol.5
New Mutants #39 [6] New Mutants Omnibus, vol.2
New Mutants Epic Collection, vol.3: Asgardian Wars
New Mutants Classic, vol.5
New Mutants #40 [6] New Mutants Omnibus, vol.2
New Mutants Epic Collection, vol.3: Asgardian Wars
New Mutants Classic, vol.5

Footnotes:

  1. Takes place during Secret Wars II #1, as the Beyonder wears the form of the Molecule Man in this story.
  2. This issue is also a part of the Scourge of the Underworld event.
  3. Placed here as a best fit, since it is not clear where it would actually take place. Or what the point of it is.
  4. These issues were not reprinted in the Secret Wars II Omnibus due to rights issues.
  5. These two issues take place during Secret Wars II #8, as specified in that issue.
  6. Deals with the fallout of New Mutants #37.