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This is the first part of the massive X-Men map.  It starts with Giant Size #1, because everything prior to that is fairly straightforward, and I think most people are getting those issues via Marvel Masterworks.   I’ll post each section of the complete map as I get them finalized.
I don’t do volume numbers for three reasons:
1.) this was a long project, and I did not bind the volumes in order. I continued to refine the map as I was already sending other books in.
2.) I didn’t know how to count crossovers, since they could be seen as volumes in multiple series.
3.) I used officially produced TPBs and hardcovers in various places, which I was not able to contribute my own number to.

I’ll list the X-Factor volumes in this map, for chronological placement purposes, but for the full map of those books, go to this link:  X-Factor (original team)

Also, I am not binding New Mutants.  If I was, I would probably structure things differently, especially around UXM #167.

The first few volumes are constructed with issues of Classic X-Men.  If a Classic X-Men issue is listed in the map, I’m referring to the backup story.  I’ll refer to the main story by its proper issue number.  Page numbers from an issue of Uncanny (for when an issue is spliced) are referring to the pages in the Classic X-Men reprint, which might be different due to the additional material.

The early volumes were originally designed as standalone books.  Later on, I came up with an alternate map, seen at the bottom of this post.

Second Genesis
Classic X-Men #1 (pg 1-4)
Giant Size X-Men #1 (chap 1)
Giant Size X-Men #3
Giant Size X-Men #1 (chap 2-4)
Classic X-Men #1 (pg 19-32)
UXM #94 (chap 1) [includes all extra material from CXM #2]
Giant Size X-Men #4
Classic X-Men #2 (Storm/Jean)
UXM #94 (chap 2)
UXM #95
Classic X-Men #3 (Thunderbird’s funeral)
UXM #96
Classic X-Men #4 (Nightcrawler/Wolverine)
Classic X-Men #5 (Colossus)
Classic X-Men #10 (Wolverine vs. Sabretooth)
Classic X-Men #11 (Storm and the suicidal writer)
Classic X-Men #15 (Starjammers)

I used the Special Edition X-Men reprint for the Giant Size #1.  That way, I was able to use the brand new back up story in a future volume.  I also used the Giant Size #4 reprints for parts of #94, all of #95, and Classic X-Men #3.  Finally, I used What If? #9 and #23 to pad out the volume.

Phoenix Saga
CXM #14 (Lilandra)
UXM #97
CXM #6 (Jean Grey’s date night)
UXM #98-100
CXM #8 (origin of Phoenix)
UXM #101 (pg 1-9)
CXM #7 (Hellfire Club New Year’s)
CXM #9 (Nightcrawler in hospital)
UXM #101 (pg 10-20)
UXM #102-104
CXM #13 (Phoenix/Misty Knight)
UXM #105-108
CXM #12 (Magneto)

I probably should have moved the CXM #7 backup to a different place, possibly somewhere in the middle of UXM #99, but I’m not completely sure where that story would really work.

The Odyssey
UXM #109
CXM #26 (Wolverine’s bar story)
CXM #28 (costume party)
UXM #110
CXM #18 (Phoenix and Wolverine camping)
CXM #27 (Cyclops, Phoenix, Wolverine, and creatures)
CXM #17 (Mesmero)
UXM #111-113
UXM #114 (p. 1-12)
CXM #21 (Colossus in the Savage Land)
UXM #114 (p. 13-21)
UXM #115
UXM #116 (p. 1-17)
CXM #22 (Storm in the Savage Land)
UXM #116 (p. 18)
UXM #117
CXM #23 (Nightcrawler’s High Adventure)
CXM #24 (Phoenix’s Vacation)
UXM #118-121
CXM #25 (Wolverine hunting)
CXM #20 (Storm’s nightmare)

Reality Check
UXM #122-124
CXM #30 (Arcade)
CXM #29 (Colossus in Russia)
UXM Annual #3
UXM #125
CXM #31 (Xavier and Lilandra in space)
UXM #126
CXM #32 (Nightcrawler and Wolverine during the Proteus battle)
UXM #127 (p. 1-4)
CXM #33 (Havok and Polaris)
UXM #127 (p. 5-17)
UXM #128
CXM #34 (Hellfire Club)

The backups from Classic X-Men #18, 20, 25-28, and 30-34 were not written by Claremont.

Dark Phoenix
UXM #129-137

Days of Future Past
UXM #138
UXM Annual #4
UXM #139-143

For the previous two volumes, I just used the TPBs that Marvel made back around 2004 or so.  As a result, I don’t have a map for the CXM backups during that time.  But by this point, they were quickly sliding into filler material more than stories that could hold their own in X-Men canon. The backups ended as the series shifted to X-Men Classic.

Going Rogue
UXM #144
Spider-Woman #37-38
UXM #145-148
Avengers Annual #10
UXM #149-150
UXM Annual #5
Bizarre Adventures #27 (Phoenix story)

I goofed on my first attempt to bind this one.  I thought I did my research, and a lot of places list Avengers Annual #10 as taking place between UXM #149-150.  However, actually reading the stories proves that to be impossible.   Just look at Kitty Pryde’s costume that she debuts in #149…she’s still wearing it in #150, and the X-Men are on the same Blackbird flight.  But, rebinding gave me the option to include Spider-Woman #37 and #38  – which I got in reprint form when I picked up Giant Size Spider-Woman #1 for a New Avengers book - which feature Siryn, a plot point picked up on in #148.  Beware of the Avengers Annual #10 reprint that came with the Marvel Legends action figure; it cuts out 9 pages of story, most of it being Rogue’s plot.  In fact, the reprint reduces her down to about 4 panels.  Finally, the Bizarre Adventures story was reprinted in color in December 2017 in the True Believers: Phoenix – Bizarre Adventures one-shot.

The Marvel Fanfare arc (#1-4) with Spidey and the X-Men in the Savage Land, available in TPB, goes here.

Live Free or Die
UXM #151-153
X-Men Unlimited #29 (bu)
UXM #154-167
UXM Annual #6
Special Edition X-Men #1 (bu)
God Loves, Man Kills

Here’s where the Special Edition backup comes into play.  The XMU backup isn’t necessary, but if you’re binding all the way through, you need some place to put it.  This is a large volume, mainly because there is no way to break the story anywhere between #154 and 167.  Also, reprint hunters, beware of X-Men Archives featuring Legion #4, which reprints UXM #161.  It skips the last two pages of the story.  UXM Annual #6 is available in X-Men vs. Dracula #1.

From the Ashes
UXM #168-171
Wolverine #1-4
UXM #172-173
X-Men:  Gold #1 (50th Anniversary special, lead story only)
UXM #174-176

Strange Tales
UXM Annual #7
Marvel Team-Up #135 (Kitty Pryde and Spider-Man)
UXM #177-179
X-Men vs Micronauts #1-4
NM #14
UXM #180
NM #15-17

The New Mutants issues are included to complete the Kitty subplot from UXM #180.  Also, a volume break was placed here because Secret Wars takes place between UXM #180-181, and that seems to be a great place for a volume break.

The Past of Future Days
UXM #181-184
Marvel Fanfare #40 (second story)
UXM #185-191

I bought Marvel’s Premiere hardcover of Kitty Pryde and Wolverine and placed it between these volumes.  The events are alluded to a few times at the end of “The Past of Future Days”, but the mini has to take place before UXM #192, when Kitty and Wolverine return to the team.

Worlds of Adventure
UXM #192 (p. 1-21)
X-Men Annual #8
X-Men/Alpha Flight #1-2
UXM #192 (p. 21-23)
UXM #193-199
NM Special Edition #1
UXM Annual #9
UXM #200-201

Yes, I spliced UXM #192 in the middle of a page.   The caption “Columbia University, New York City, some months later…” is the split point.

—-X-Factor:  Phoenix Rising goes here.

Retribution
UXM #202-209

Mutant Massacre
X-Factor #8-9
UXM #210
NM Annual #2
UXM Annual #10
UXM #211
X-Factor #10
NM #46
Thor #373
Power Pack #27
Thor #374
UXM #212
X-Factor #11
DD #238
UXM #213
X-Factor #12-15

I’m not one of those that likes to keep X-Men and X-Factor separate during the Massacre.

Old Soldiers
UXM #214-219
FF vs. X-Men #1-4
X-Men vs. Avengers #1-4
X-Factor Annual #4 (bu – Doom vs. Magneto)

Fall of the Mutants
UXM Annual #11
UXM #220-227

It is not necessary to include any other Fall of the Mutants issues, because each of the three X-series had separate storylines for this “event.”

—-two X-Factor volumes go here:  Fall of the Mutants, and Kiss of Death

Down Under
UXM #228-234
UXM Annual #12
UXM #235-238

Annual #12 is part of the Evolutionary War.  I have the EW omnibus to read that story as a whole, but many of the annuals work well separated into their parent series.

Inferno
X-Factor #33
X-Terminators #1
X-Factor #34
X-Terminators #2
UXM #239
X-Factor #35-36
UXM #240
X-Terminators #3
NM #71
X-Terminators #4
NM #72
UXM #241
X-Factor #37
NM #73
UXM #242
X-Factor #38
UXM #243
X-Factor #39
X-Factor Annual #4 (Inferno aftermath backup)
X-Factor #40

This is the official Marvel HC that came out in 2009.  If binding, I would offer an alternative and move New Mutants #73 to before X-Factor #37, so that the direct continuation of X-Factor #37 to UXM #242 is intact.

—-X-Factor:  Judgement War takes place here

Siege Perilous
UXM #244
UXM Annual #13 (b/u)
UXM #245-269

The main story of UXM Annual #13 is part of Atlantis Attacks.  I’m saving that for it’s own bind and not worrying about trying to place those annuals in the context of their main series.   Originally, I was going to do this as two volumes, split somewhere around the Acts of Vengeance arc in #256-258, but for the sake of being cheap, just made one large book.

—-X-Factor:  The Raven Saga goes here.

Days of Future Present
Fantastic Four Annual #23
NM Annual #6
X-Factor Annual #5
UXM Annual #14

—-X-Factor:  Feeling Blue goes here.

X-Tinction Agenda
UXM #270
NM #95
X-Factor #60
UXM #271
NM #96
X-Factor #61
UXM #272
NM #97
X-Factor #62
UXM #273

Kings of Pain
NM #98-100
NM Annual #7
New Warriors Annual #1
UXM Annual #15
X-Factor Annual #6

—-X-Factor:  Endgame goes here.

Crossroads
UXM #274-279
X-Factor #69
UXM #280
X-Factor #70

I originally planned to make #273-277 it’s own volume called “Crossroads”, and then have the Muir Island Saga – the rest of the issues in this volume - be it’s own book.  But, in the interest of fewer volumes, I came up with this arrangement.  This also helps the continuity, since X-Factor and the New Mutants guest star in #273.

Alternate mapping of early volumes:

When I decided to redo the early part of my collection, I tightened the map up a bit.  A lot of the Classic X-Men stories were removed when I used a trade of the Masterworks volume reprinting UXM #101-110.  Most of those stories weren’t extremely relevant, and the few that I kind of wish I could keep would have caused pacing problems anyway.  I also cut out as many non-Claremont backup stories as possible.

Second Genesis
Classic X-Men #1 (pg 1-4)
Giant Size X-Men #1 (chap 1)
Giant Size X-Men #3
Giant Size X-Men #1 (chap 2-4)
Classic X-Men #1 (pg 19-32)
UXM #94 (chap 1) [includes all extra material from CXM #2]
Classic X-Men #2 (Storm/Jean)
Giant Size X-Men #4
UXM #94 (chap 2)
UXM #95
Classic X-Men #3 (Thunderbird’s funeral)
UXM #96
Classic X-Men #4 (Nightcrawler/Wolverine)
Classic X-Men #5 (Colossus)
UXM #97
CXM #6 (Jean Grey’s date night)
UXM #98-100
CXM #8 (origin of Phoenix)
UXM #101-110

The Odyssey
CXM #17 (Mesmero)
UXM #111-113
UXM #114 (p. 1-12)
CXM #21 (Colossus in the Savage Land)
UXM #114 (p. 13-21)
UXM #115-117
CXM #23 (Nightcrawler’s High Adventure)
CXM #24 (Phoenix’s Vacation)
UXM #118-124
UXM Annual #3
CXM #29 (Colossus in Russia)

Proteus (Marvel Premiere Classic HC)
UXM #125-128
CXM #32-33, 36

This map rejoins with the Dark Phoenix Saga TPB above.

This ends the Claremont era, as next comes X-Men #1, which remixes the entire X-franchise.
The mapping continues:
X-Men 1991-1994
X-Men 1995-2001
2001-2008
Messiah Era