Think of Marvel "Ultimate" comics as a starting point for new readers. Marvel took the most popular characters and "rebooted" everything with a clean, fresh take on the world of superheroes.
In the "ultimate universe" pretty much all superheroes are tied back to the super-soldier experiments done in WWII which gave us Captain america. Lots of genetic tampering going on in various labs and research centers which give rise to the various heroes and villains that crop up.
As mentioned above, the "ultimate" spider-man is bitten by an escaped genetically enhanced spider that manages to transfer the powers through a bite where the venom pretty much rewires some of Pete's genetic code and tacks on the spider powers.
Moving out from this new starting point, we add in the X-Men and Fantastic Four series and various mini-series releases. Each one building on top of the new starting point and incorporating existing Marvel heroes and villains into the new framework. All the time we are trying to keep things grounded into the genetic-tampering mix with the minimal amount of extra-dimensional, extra-terrestrial, and magical influence as possible.
It boils down to this:
- If you are a new reader, or very light reader of Marvel comics then you have a good place to jump in and enjoy without all of the existing "baggage" inherent in the many, many years of existing back issues from the non-ultimate series.
- If you are a die-hard Marvellian, or at least are extremely well versed in the Marvel universe and its history then you have an alternative universe to poke around in and see how they have redesigned existing characters and retold existing story arcs.
Personally, I have always preferred the Marvel comics over others since I started reading them around 30 years ago and I prefer the "ultimate" universe overall.
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