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This map is designed to bind the first 70 issues of X-Factor, but still have volume breaks where it is convenient to bounce back and forth between X-Factor and X-Men.  Yes, there are some small volumes.

X-Factor:  Phoenix Rising
Avengers #263
Fantastic Four #286
X-Factor #1-4
X-Factor Annual #1
X-Factor #5-7

X-Men/X-Factor:  Mutant Massacre
X-Factor #8-9
UXM #210
New Mutants Annual #2
UXM Annual #10
UXM #211
X-Factor #10
New Mutants #46
Thor #373
Power Pack #27
Thor #374
UXM #212
X-Factor #11
Daredevil #238
UXM #213
X-Factor #12-15

The two annuals are included as part of my comprehensive X-Men project.  If you’re just doing X-Factor, you can skip them.

X-Factor:  Fall of the Mutants
X-Factor #16
Thor #377-378
X-Factor#17-20
Hulk #336-337
X-Factor Annual #2
X-Factor #21-26

For Thor #377, I only used two pages that showed Iceman being captured, and in Thor #378, I cut out any pages that didn’t tie directly into the plot with Iceman.  Some like to use all of #377-379, but that’s a bit overkill for an X-Factor book.

X-Factor:  Kiss of Death
X-Factor #27-29
X-Factor Annual #3
X-Factor #30-32

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.  Also, the main story of Annual #4 goes in an Atlantis Attacks volume, which the Doom/Magneto backup goes in a volume with the X-Men vs Avengers mini-series.

X-Factor:  Judgement War
X-Factor #41-50

X-Factor:  The Raven Saga
X-Factor#51-58

I probably could have combined these into one volume.

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

The NM Annual is listed as part 3, and X-Factor as part 2. As explained on the first page of the NM Annual, it was originally scheduled to be part 2, but it was running late, so they released X-Factor first. The proper reading order is what I have listed above, even though it looks like parts 1, 3, 2, 4.  Another alternative is getting the Days of Future Past OHC which contains this crossover along with the original arc and several other related and spin-off issues.

X-Factor:  Feeling Blue
X-Factor #59
Prisoner of Love
X-Factor Annual #5 (bu)
MCP #85-92 (Beast story)
Marvel Fanfare #50

A sort of catch-all book, but necessary, since #59 clearly takes place between Days of Future Present and X-Tinction Agenda, but doesn’t really fit well with either book.

X-Tinction Agenda
Uncanny X-Men #270
New Mutants #95
X-Factor #60
Uncanny X-Men #271
New Mutants #96
X-Factor #61
Uncanny X-Men #272
New Mutants #97
X-Factor #62
Uncanny X-Men #273

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

X-Factor:  Endgame
X-Factor #63-68

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