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Previously…
Uncanny X-Men #94-280
X-Men 1991-1994
Age of Apocalypse

During this era, I start skipping some annuals and issues of X-Men Unlimited.  Most of them either aren’t good, or don’t fit in (or both).  I included the Wolverine series from #91-100, because #100 is a big issue, and the issues between that and AoA are all pretty much the lead up, and feature quite a bit of other X-Men.

Prime
X-Men:  Prime
Cable #21
UXM #322
X-Men #42-44
X-Force #44
Wolverine #91
UXM #323-324
Wolverine #92-93
UXM #325
X-Men ’95
Wolverine #94
X-Men #45
UXM ‘95

Evil Natures
UXM #326
X-Men #46-47
Wolverine #95
UXM #327
Wolverine #96
UXM #328
Sabretooth
X-Men #48
UXM #329-330

Cable/X-Man:  The Man in the Mirror
X-Man #5-7
Cable #22-25
X-Man #8-11
Cable #26-28
X-Man #12
Excalibur #95
Cable #29
X-Man #13
Cable #30
X-Man #14
Cable #31

(Since there are a few key moments in these issues during the lead up to Onslaught, I opted to go all the way up to the Cable/X-Man crossover, and put it in its own book.  Cable #21 had to go in the Prime volume, because it takes place before X-Force #44.  I’m not interested enough in X-Man to worry about getting the few issues between this book and Onslaught.)

The Road to Onslaught
X-Men #49
XMU #10
X-Men #50
UXM #331
X-Men #51-52
X-Men #53 (pg. 23 – the page with Joseph in Carolina)
Wolverine #97-100
UXM #332
Wolverine #101
Cable #32
UXM #333
X-Force #55
XMU #11
Cable #33

(I included that one page from X-Men #53 in the midst of X-Men #52, because it has to go before XMU #11.)

Onslaught
X-Men #53
UXM #334
X-Men #54
Onslaught: X-Men
UXM #335
X-Factor #125
Cable #34
Hulk #444
Avengers #401
Wolverine #104
Excalibur #100 (Xavier Protocol pages only)
FF #415
X-Man #18
X-Force #57
X-Men #55
UXM #336
Cable #35
X-Factor #126
ASM #415
Spider-Man #72
X-Man #19
FF #416
Hulk #445
Iron Man #332
Avengers #402
X-Men #56
Onslaught:  Marvel Universe

(I included the back up from FF #416 at the end of this book, for lack of a better place to put it.)

Onslaught Aftermath
Cable #36
UXM #337
X-Men #57
UXM #338
X-Men #58
UXM #339
X-Men #59
X-Men ’96
Onslaught:  Epilogue
X-Men:  The Road to Onslaught

(Amazing Spider-Man #416 can be included after UXM #337, if you’re so inclined.)

Death and Deceit
UXM #340
X-Factor #130
X-Men #60-61
XMU #14
X-Men ’97
Beast #1-3
UXM #341-345
X-Men #62-64

Operation:  Zero Tolerance
X-Men #65
UXM #346
Cable #45-47
X-Men #66
Wolverine #115
UXM #347 (3 pages with Callisto and Marrow)
X-Men #67-68
Wolverine #116-118
X-Men #69
UXM #347-350
X-Men #70

A House in Order
X-Men #71
UXM #351-352
XMU #18 (bu)
XMU #17
X-Men #72
UXM #353-354
X-Men #73
UXM #355
Cable/Machine Man ’98
Machine Man/Bastion ‘98
XMU #18

Life Lessons
X-Men #74-75
UXM #356-357
X-Men #76-78
UXM #358-359
UXM/FF ’98
X-Men #79
XMU #21

The Hunt for Xavier
UXM #360
X-Men #80
UXM #361
X-Men #81
UXM #362
X-Men #82
UXM #363
X-Men #83
UXM #364
X-Men #84
UXM #365
XMU #22
X-Men #1/2

Magneto War
X-Men #85
Magneto War #1
UXM #366
X-Men #86
UXM #367
X-Men #87
UXM #368
Magneto Rex #1-3
XMU #24 (back-up)

Warped Realities
X-Men #88
UXM #369
X-Men #89
UXM #370
X-Men #90
UXM #371
X-Men #91
X-Men ’99
XMU #23-24
X-51 #0

The Shattering
UXM #372
X-Men #92
Gambit #8-9
UXM #373-374
X-Men #93-94
AXM #1-3
UXM #375
X-Men #95
XMU #25
Wolverine #145
Cable #73-74

Apocalypse:  The Twelve
UXM #376
Cable #75
X-Men #96
Wolverine #146-147
UXM #377
Cable #76
UXM ’99
X-Men #97
UXM #378
Cable #77
Wolverine #148
XMU #26
X-Men #98

Mutants No More
Cable #78
UXM #379
X-Men #99
UXM #380
Gambit #10-15
XMU #27
XMU #25-26 (bu)

Black Sun
Black Sun #1-5

(This mini-series takes place sometime prior to X-Men #100, in the six month gap era. However, it just doesn’t seem right to put it in the same book as X-Men #100, and it also doesn’t fit well with the previous volume.)

Cable: Undying
Cable #79-86

(This and the next Cable volume aren’t vital to the overall X-Men chronology, but I really liked Robert Weinberg’s run, and was really irritated when Marvel decided to remove him from the book. I’m including those books here, just to show where they fall in the chronology. The entire run fits in two books, with one issue in the Dream’s End volume.)

Revolution
X-Men #100-102
UXM #381-383
X-Men Unlimited #28 (main story)
X-Men #103
UXM #384
X-Men #104
UXM #385
X-Men 2000
X-Men #105
X-Men Forever #1-6
X-Men #106
UXM #386

There are several things I need to address with this volume.
1.) Yes, this is a big volume. I wanted to not include X-Men Forever and make that it’s own book, but it has to take place before X-Men #106, which is the end of the whole Neo thing that had started in #100. It didn’t make much sense splitting the Neo arc up. But for those really worried about size, this book is about the same thickness as the complete run of X-Men: Hidden Years, which many people do as a done in one.
2.) Cardstock covers on Forever. Kind of sucks, but I only included the front covers. I retyped the info from the back covers and printed it out. Really, the covers only cause issues with pages not laying down during those actual issues.
3.) Continuity is fudged a bit. Since Claremont and editorial were butting heads over pacing and scheduling (thanks to the first X-Men movie), some of the stories don’t really flow well. One point is X-Men Annual 2000. It has Rogue as team leader, although she didn’t officially get that position until X-Men #103, which goes directly into the crossover in UXM #384/X-Men #104/UXM #385. But then there were events in that arc that make certain bits of the annual not make sense. I do believe I asked Claremont on the X-Fan message boards years ago, and basically said something along the lines that the annual might as well fit in there. As for UXM #386, because the team starts #387 in the same place they ended #386, it makes sense to put it after the Neo conclusion in X-Men #106.
4.) X-Men Unlimited #27 is about Thunderbird III joining the X-Men. I’m including that in the Mutants No More volume that will go just prior to the books on this list to help increase the size of that volume.
5.) The backup story from XMU #28 is a Deadpool solo story, and should go into a Deadpool volume, not in a main X-Men volume.
6.) If my first two notes bother you, skip X-Men Forever. It will decrease the size of the book greatly, and eliminate the cardstock cover issue. Also, it can help the pacing, but as I think about it, XMF was a time travel story, so the characters were plucked out of time, and then returned.

Maximum Security
MS: Dangerous Planet
MS #1
UXM #387
Bishop #15
MS #2
X-Men #107
XMU #29 (main story)
Avengers #35
MS #3

More notes:
1.) I only did an X-Men-centric volume for this Marvel-wide crossover. I wasn’t interested in enough of the other characters and series at the time to bother with hunting them down. The only other series I was following regularly at the time was Fantastic Four, and it didn’t tie in.
2.) That said, I usually get any tie-ins written by the main writer, hence the Avengers issue.
3.) The editor’s notes at the beginning of several issues indicating reading order are not always right. I think X-Men #107 is the main culprit.
4.) The backup from XMU #29 was put into a much earlier volume, circa Uncanny #152-153.

Dream’s End
UXM #388
Cable #87
Bishop #16
X-Men #108
UXM #389
X-Men #109
UXM 2000
X-Men #390
X-Men #110
XMU #30 (all except the first story)

(The first story in XMU #30 is a Generation X story, which is why I skipped it.)

Cable: Dark Sisterhood
Cable #88-96

(For those purists about Cable and Weinberg’s run, this is the best place to break it, even if one issue ends up in a larger X-Men volume. As it turns out, I believe someone else ghost wrote large chunks of Cable #87. And the run still reads decently if you only read Cable and skip #87.)

Eve of Destruction
Search for Cyclops #1-4
UXM #391
X-Men #111
UXM #392
X-Men #112
UXM #393
X-Men #113

Gambit/Bishop: Sons of the Atom
Gambit #25
Gambit/Bishop Alpha
Gambit/Bishop #1-6

Continued:
2001-2008
Messiah Era