X-MEN

(Post X-Factor, Scott and Jean appear in the X-Men series and Uncanny X-Men series simultaneously, in the sections "X-Men" and "Uncanny X-Men" respectively.)
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#12

(X-cutioner's Song)
#14
X-Force #16
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X-Force #17
#16
X-Force #18

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#24

(Fatal Attractions)
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Wolverine #75
Excalibur #71

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#30
(Optional to proceed with The Adventures of Cyclops and Phoenix miniseries.)
(Optional to proceed with The Further Adventures of Cyclops and Phoenix miniseries.)
#35
X-Men Unlimited #6

(Phalanx Covenant)
Wolverine #85
Cable #16

#38
Cable #17
#39

(Legion Quest)
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#41
Cable #20
(Proceed with Age of Apocalypse before continuing below.)

#42
Wolverine #91
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X-Force #55
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#53

(Onslaught)
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Onslaught: X-Men
Excalibur #100
#56
X-Men Unlimited #12
Onslaught: Marvel Universe

#57
#59
X-Men Unlimited #13
#61
Wolverine #111
#62
#63
#64
Cable #44

(Operation: Zero Tolerance)
#65
#66
Wolverine #115
Wolverine #116
Wolverine #117
Wolverine #118

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#71
The Magneto War #1
#88
#92
(Proceed with The Astonishing X-Men (2nd Series) miniseries before continuing below.)

#95

(The Twelve)
#96
Cable #96
#97

(Ages of Apocalypse)
#98
(Proceed with The Search for Cyclops miniseries before continuing below.)

(Eve of Destruction)
#113

(Stand alone titles)
The Wedding Album
Marvel Valentine Special
Marvel Holiday Special

NEW X-MEN

(After the Eve of Destruction arc, Marvel decided to rename the X-Men series to New X-Men. Chronologically New X-Men picks up where X-Men left off, just a change in title.)

(E is for Extinction)
#114
#116
New X-Men Annual 2001
#117

(Imperial)
#118
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#126

(New Worlds)
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#130

(Riot at Xavier's)
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#138

(Murder at the Mansion)
#139
#140

(Assault on Weapon Plus)
#142

(Planet X)
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#150

(Here Comes Tomorrow)
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#154

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#157

ASTONISHING X-MEN VOL 3

(I know Astonishing X-Men is a separate series run branching off from the New X-Men series, renamed back to X-Men, but I'm not putting the entire run here, just a few Scott and Jean loose ends that appeared early on in Astonishing X-Men. For what it's worth, Joss Whedon writes an amazing Kitty Pryde, the only saving grace in this series IMO.)
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X-MEN: LEGACY

(After New X-Men, X-Men Vol. 2 is renamed X-Men: Legacy.)
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