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Top 50 Marvel Comics of the 2000s

There were a few (well at the top of my head, Slott's Amazing Spider-Man, Remender's Punisher, Hickman's Secret Warriors, and Hickman's Fantastic Four) runs where the majority of it and its peaks were in the 2010s despite having a few issues released in 2008/2009 so they have been disqualified. And remember kids, origin stories are stupid!
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avg. score: 6 of 50 (13%)
required scores: 1, 2, 3, 6, 13 
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1
Agents of Atlas (Jeff Parker)
Agents of Atlas (Jeff Parker)
2
Alias (Brian Michael Bendis and Michael Gaydos.)
Alias (Brian Michael Bendis and Michael Gaydos.)
3
Amazing Spider-Man (Straczynski) (J. Michael Straczynski)
Amazing Spider-Man (Straczynski) (J. Michael Straczynski)
4
Annihilation
Annihilation
5
Annihilation: Conquest
Annihilation: Conquest
6
Astonishing X-Men (Joss Whedon & John Cassidy)
Astonishing X-Men (Joss Whedon & John Cassidy)
7
Brian Michael Bendis' Avengers
Brian Michael Bendis' Avengers
8
Stormbreaker: The Saga of Beta Ray Bill (2005) #1 (March 2005)
Stormbreaker: The Saga of Beta Ray Bill (2005) #1 (March 2005)
9
Cable & Deadpool
Cable & Deadpool
10
Ed Brubaker's Captain America
Ed Brubaker's Captain America
11
Captain Marvel (Peter David)
Captain Marvel (Peter David)
12
Civil War (Mark Millar)
Civil War (Mark Millar)
13
Daredevil: Brian Michael Bendis Run (Daredevil #26 to #50, #56-81)
Daredevil: Brian Michael Bendis Run (Daredevil #26 to #50, #56-81)
14
Daredevil: Ed Brubaker's Run (Daredevil #82 to #119)
Daredevil: Ed Brubaker's Run (Daredevil #82 to #119)
15
Exiles #1-#37 (Judd Winick, Mike McKone)
Exiles #1-#37 (Judd Winick, Mike McKone)
16
Iron Man: Extremis (Warren Ellis)
Iron Man: Extremis (Warren Ellis)
17
Fantastic Four (Mark Waid & Mike Wieringo)
Fantastic Four (Mark Waid & Mike Wieringo)
18
Guardians of the Galaxy #1-#25 (Dan Abnett, Andy Lanning)
Guardians of the Galaxy #1-#25 (Dan Abnett, Andy Lanning)
19
House of M (Brian Michael Bendis)
House of M (Brian Michael Bendis)
20
Immortal Iron Fist (Matt Fraction)
Immortal Iron Fist (Matt Fraction)
21
Incredible Hercules #113-#141 (Greg Pak, Fred Van Lente, Paul Neary)
Incredible Hercules #113-#141 (Greg Pak, Fred Van Lente, Paul Neary)
22
Invincible Iron Man (#1-33; 500-527) (Matt Fraction & Salvador Larroca)
Invincible Iron Man (#1-33; 500-527) (Matt Fraction & Salvador Larroca)
23
The Irredeemable Ant-Man (Robert Kirkman)
The Irredeemable Ant-Man (Robert Kirkman)
24
Marvel Knights Spider-Man by Mark Millar (Marvel Knights: Spider-Man #1-12)
Marvel Knights Spider-Man by Mark Millar (Marvel Knights: Spider-Man #1-12)
25
X-Men: Messiah Complex (Ed Brubaker)
X-Men: Messiah Complex (Ed Brubaker)
26
New X-Men (Grant Morrison)
New X-Men (Grant Morrison)
27
Nextwave: Agents of H.A.T.E. (Warren Ellis and Stuart Immonen)
Nextwave: Agents of H.A.T.E. (Warren Ellis and Stuart Immonen)
28
Nova (Dan Abnett)
Nova (Dan Abnett)
29
Planet Hulk (Incredible Hulk #92-#105) (Greg Pak, Carlo Pagualyan)
Planet Hulk (Incredible Hulk #92-#105) (Greg Pak, Carlo Pagualyan)
30
Punisher (Garth Ennis)
Punisher (Garth Ennis)
31
Runaways (Brian K.Vaughan)
Runaways (Brian K.Vaughan)
32
Secret War (Brian Michael Bendis)
Secret War (Brian Michael Bendis)
33
Sentry #1-#5 (Paul Jenkins, Jae Lee)
Sentry #1-#5 (Paul Jenkins, Jae Lee)
34
Son of M (David Hine)
Son of M (David Hine)
35
Supreme Power (2003) (J. Michael Straczynski)
Supreme Power (2003) (J. Michael Straczynski)
36
Thor (J. Michael Straczynski)
Thor (J. Michael Straczynski)
37
Thunderbolts (Warren Ellis)
Thunderbolts (Warren Ellis)
38
Ultimate Galactus Trilogy (Warren Ellis)
Ultimate Galactus Trilogy (Warren Ellis)
39
Ultimate Spider-Man
Ultimate Spider-Man
40
Ultimate X-Men
Ultimate X-Men
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