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The Best Marvel Comics Stories of the 00s

An interesting thing happened in the comic book industry. The 80s are known for long boxes full of iconic, wonderful stories.

Then, the 90s were the boom in the industry. Millions upon millions of comic books were being sold, making creators rich. Yet few of those 90s stories were actually any good. Maybe entertaining. Likely “edgy” or “xtreme.” But rarely good.

But the pendulum swung back. 00s comics were good again! Unlike the 90s list, where I had to reach to recommend 7 storylines, the 80s list was me agonizing over how to limit the list to 7.

Once again, preparing this 00s list was agony. A story as memorable and iconic as Civil War didn’t even make the cut, which tells you that many more deserving 00s Marvel comics didn’t make this list of the best.

That the below 7 did should tell you something. So let’s turn the page and start reading.

Captain America: “Winter Soldier”

In 2005, Marvel published vol 5 of Captain America with Ed Brubaker at the helm. The 50 issues of the series would come to redefine the history of the character, propelling it forward into the movies of the MCU.

The series was best known for its “Winter Soldier” arc, followed by the “Death of Steve Rogers.” We’ve seen the movies and have grown to know the character Bucky Barnes, Ed Brubaker was the one that made him relevant.

Again, Marvel comics were really good during this period and Captain America was written in the era of Civil War. Yet, “Winter Soldier” (and indeed the full 50 issue run) still stands out as a great storyline of the 00s.

Here’s the Winter Soldier arc collected, but consider the full 50 issue run.


Before the Guardians of the Galaxy movie became a world-wide hit in 2014, casual fans likely didn’t realize that Marvel Comics contained a rich, vibrant catalog of amazing “cosmic” characters and decades of astonishing stories set in the vastness of space. 

Sure, casual fans likely had a passing understanding that Iron Man or Captain America sometimes battled aliens and Thor didn’t grow up in Spider-Man’s friendly neighborhood, but most had their minds’ blown by the likes of Rocket Raccoon and Groot. 

Indeed, Marvel Comics has a galaxy of characters rivaled perhaps only by the Star Wars franchise. This came to the fore in Annihilation. Operating on the fringe of Marvel Comics–and simultaneous with the Civil War event–Annihilation wasn’t a huge seller at release. But word of mouth brought in an audience who were hooked after reading.

I love Annihilation so much I wrote an issue-by-issue reading order for you. And here’s where to buy the first collected edition.

Incredible Hulk: “Planet Hulk”

You’ll notice a couple of crossover events on this list, but what is really appreciated is how many great stories were told within the pages of Marvel’s regular monthly series. Planet Hulk is one such storyline.

MCU fans saw a version of the story in Thor: Ragnarok. In the comic, a group of Marvel heroes send the Hulk away, deeming him too violent and unpredictable to remain on Earth. The Hulk acclimates to the planet where he landed, eventually conquering it in gladiatorial combat. He then returns to Earth to take his revenge.

Written by Greg Zak, the storyline includes Incredible Hulk #92–105 and Giant-Size Hulk #1.

Here’s the collection.

Wolverine: “Old Man Logan”

Old Man Logan is an aged version of Wolverine set in an alternate future.  It was published as an 8-issue storyline from the Wolverine ongoing comic by writer Mark Millar and artist Steve McNiven in 2008. The storyline ran through Wolverine #66–72 and culminated in Wolverine Giant-Size Old Man Logan #1.

We written about Old man Logan before, so I’ll point you there if you want a greater introduction.

It’s an imaginative as well as deeply entertaining story. The character proved so popular with fans that Old Man Logan was brought into the 616 and received his own series.

Get the hardcover collection, it was certainly one of the best Marvel storylines of the 00s.

Astonishing X-Men

X-Men comics were an absolute mess at the turn of the Millennium. Grant Morrison brought new life to the line with his New X-Men in 2001, yet it was controversial. Many fans hated it, many (including me) loved it, and Marvel ultimately rolled back most of the storylines he wrote. The X-Men comics that followed like Chuck Austen’s X-Men were an absolute embarrassment.

Yet there is one X-Men story from the 00s that is near universally praised as being among the absolute best for the decade: Joss Whedon’s Astonishing X-Men.

Running 24 issues plus a Giant-Sized, it was nothing sort of astonishing. We’ve written about it before and shared our favorite moments.

You can pre-order the collected version here.


Sometimes the best comics take existing characters in a wholly new direction, under new circumstances. Sometimes the best introduce brand new characters all together.

Written by Brian K Vaughan, Runaways begins as a group of teenagers–Nico, Karolina, Molly, Alex, Gertrude, and Chase–are hanging out at one of their parents’ work holiday party.

But it quickly changes as the group discovers that their parents, all of their parents, are super villains. From there, the group lives up to their namesake running away from home and working to defeat their evil parents.

We’ve written more about Runaways, including how Charles Manson anxieties contribute to the series.

It’s an excellent comic that is absolutely among Marvel’s best of the 00s. The first 18 issues are collected here.

House of M

We close this list of the best Marvel comics of the 00s with a crossover that not only introduced one of the most iconic panels in comic book history, but also changed the trajectory of the X-Men for over a decade.

An 8-issue series, House of M featured Scarlett Witch, who was rapidly losing her mind. Stricken by grief and having fully slipped into insanity, Scarlett Witch uttered the words “No more Mutants.” With her considerable powers, those words depowered nearly all of Earth’s mutants.

It was a great storyline on its own but the real legacy is that it reshaped the editorial direction of the X-Men, inspiring storylines for years afterward.

If you’ve never read, you owe it to yourself to do so. It’s collected here.

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