Jonathan Hickman's Marvel (2009-2015)

If you are only interested with the build up to Secret Wars (2015) then start at New Avengers Vol. 3 #1 (2013).  Once this list moves on to Avengers and the build up to Secret Wars (2015) select issues by other writers are included if they help create a more complete picture of events.

Dark Reign: New Nation #1 (2009)

Secret Warriors #1 (2009)
Secret Warriors #2
Secret Warriors #3
Secret Warriors #4
Secret Warriors #5
Secret Warriors #6

Dark Reign: Fantastic Four #1 (2009)
Dark Reign: Fantastic Four #2
Dark Reign: Fantastic Four #3
Dark Reign: Fantastic Four #4
Dark Reign: Fantastic Four #5

Dark Reign: The Cabal #1 (2009)

Secret Warriors #7
Secret Warriors #8
Secret Warriors #9

Dark Reign: The List: Secret Warriors #1 (2009)

Secret Warriors #10
Secret Warriors #11
Secret Warriors #12
Secret Warriors #13
Secret Warriors #14
Secret Warriors #15
Secret Warriors #16

Fantastic Four #570
Fantastic Four #571
Fantastic Four #572
Fantastic Four #573
Fantastic Four #574
Fantastic Four #575
Fantastic Four #576
Fantastic Four #577
Fantastic Four #578

S.H.I.E.L.D. #1 (2010)
S.H.I.E.L.D. #2
S.H.I.E.L.D. #3
S.H.I.E.L.D. #4
S.H.I.E.L.D. #5
S.H.I.E.L.D. #6

Fantastic Four #579
Fantastic Four #580
Fantastic Four #581
Fantastic Four #582

Siege: Secret Warriors #1 (2010)

Secret Warriors #17
Secret Warriors #18
Secret Warriors #19
Secret Warriors #20
Secret Warriors #21
Secret Warriors #22

Fantastic Four #583
Fantastic Four #584
Fantastic Four #585
Fantastic Four #586
Fantastic Four #587
Fantastic Four #588

Secret Warriors #23
Secret Warriors #24
Secret Warriors #25
Secret Warriors #26
Secret Warriors #27
Secret Warriors #28

S.H.I.E.L.D. Vol. 2 #∞
S.H.I.E.L.D. Vol. 2 #1 (2011)
S.H.I.E.L.D. Vol. 2 #2
S.H.I.E.L.D. Vol. 2 #3
S.H.I.E.L.D. Vol. 2 #4
S.H.I.E.L.D. Vol. 2 #5
S.H.I.E.L.D. Vol. 2 #6

FF #1 (2011)
FF #2
FF #3
FF #4
FF #5
FF #6
FF #7
FF #8
FF #9
FF #10
FF #11

Fantastic Four #600

FF #12

Fantastic Four #601

FF #13

Fantastic Four #602

FF #14

Fantastic Four #603

FF #15

Fantastic Four #604

FF #16

Fantastic Four #605
Fantastic Four #605.1
Fantastic Four #606

FF #17
FF #18

Fantastic Four #607
Fantastic Four #608

FF #19
FF #20
FF #21

Fantastic Four #609
Fantastic Four #610

FF #22

Fantastic Four #611

FF #23

Read Avengers vs. X-Men here.

New Avengers Vol. 3 #1 (2013)
New Avengers Vol. 3 #2
New Avengers Vol. 3 #3

Avengers Vol. 5 #1 (2013)
Avengers Vol. 5 #2
Avengers Vol. 5 #3
Avengers Vol. 5 #4
Avengers Vol. 5 #5

New Avengers Vol. 3 #4
New Avengers Vol. 3 #5
New Avengers Vol. 3 #6

Avengers Vol. 5 #6
Avengers Vol. 5 #7
Avengers Vol. 5 #8
Avengers Vol. 5 #9
Avengers Vol. 5 #10
Avengers Vol. 5 #11

Thanos Rising #1 (2013)
Thanos Rising #2
Thanos Rising #3
Thanos Rising #4
Thanos Rising #5

Guardians of the Galaxy Vol. 3 #0.1 (2013)
Guardians of the Galaxy Vol. 3 #1
Guardians of the Galaxy Vol. 3 #2
Guardians of the Galaxy Vol. 3 #3
Guardians of the Galaxy Vol. 3 #4

Avengers Vol. 5 #12
Avengers Vol. 5 #13

Guardians of the Galaxy Vol. 3 #5
Guardians of the Galaxy Vol. 3 #6
Guardians of the Galaxy Vol. 3 #7

New Avengers Vol. 3 #7

Read Infinity here.

Avengers Vol. 5 #24.NOW

New Avengers Vol. 3 #13
New Avengers Vol. 3 #14
New Avengers Vol. 3 #15

Original Sin #3.1
Original Sin #3.2
Original Sin #3.3
Original Sin #3.4

Avengers Vol. 5 #25
Avengers Vol. 5 #26
Avengers Vol. 5 #27
Avengers Vol. 5 #28

New Avengers Vol. 3 #16.NOW
New Avengers Vol. 3 #17

Avengers Vol. 5 #29
Avengers Vol. 5 #30
Avengers Vol. 5 #31
Avengers Vol. 5 #32
Avengers Vol. 5 #33
Avengers Vol. 5 #34

New Avengers Vol. 3 #18
New Avengers Vol. 3 #19
New Avengers Vol. 3 #20
New Avengers Vol. 3 #21
New Avengers Vol. 3 #22
New Avengers Vol. 3 #23

New Avengers Vol. 3 Annual #1 (2014)

Ultimate Comics Thor #1 (2010)
Ultimate Comics Thor #2
Ultimate Comics Thor #3
Ultimate Comics Thor #4

Ultimate Comics Fallout #1 (2011)
Ultimate Comics Fallout #2
Ultimate Comics Fallout #3
Ultimate Comics Fallout #4
Ultimate Comics Fallout #5
Ultimate Comics Fallout #6

Ultimate Comics Ultimates #1 (2011)
Ultimate Comics Ultimates #2

Ultimate Comics Hawkeye #1 (2011)
Ultimate Comics Hawkeye #2
Ultimate Comics Hawkeye #3
Ultimate Comics Hawkeye #4

Ultimate Comics Ultimates #3
Ultimate Comics Ultimates #4
Ultimate Comics Ultimates #5
Ultimate Comics Ultimates #6
Ultimate Comics Ultimates #7
Ultimate Comics Ultimates #8
Ultimate Comics Ultimates #9
Ultimate Comics Ultimates #10
Ultimate Comics Ultimates #11
Ultimate Comics Ultimates #12

Avengers Vol. 5 #34.1
Avengers Vol. 5 #34.2

Captain America Vol. 7 #12
Captain America Vol. 7 #13
Captain America Vol. 7 #14
Captain America Vol. 7 #15
Captain America Vol. 7 #17
Captain America Vol. 7 #18
Captain America Vol. 7 #19
Captain America Vol. 7 #20
Captain America Vol. 7 #21

Inhuman #7
Inhuman #8

Superior Iron Man #1 (2015)
Superior Iron Man #2
Superior Iron Man #3

Thor Vol. 4 #1 (2014)
Thor Vol. 4 #2
Thor Vol. 4 #3
Thor Vol. 4 #4

Avengers Vol. 5 #35

New Avengers Vol. 3 #24

Avengers Vol. 5 #36

New Avengers Vol. 3 #25

Avengers Vol. 5 #37

New Avengers Vol. 3 #26

Avengers Vol. 5 #38

New Avengers Vol. 3 #27

Avengers Vol. 5 #39

New Avengers Vol. 3 #28

Avengers Vol. 5 #40

New Avengers Vol. 3 #29

Avengers Vol. 5 #41

New Avengers Vol. 3 #30

Avengers Vol. 5 #42

New Avengers Vol. 3 #31
New Avengers Vol. 3 #32

Avengers Vol. 5 #43

Miles Morales: Ultimate Spider-Man #11
Miles Morales: Ultimate Spider-Man #12

New Avengers Vol. 3 #33

Avengers Vol. 5 #44

Read Secret Wars (2015) here.