Without constituting legal advice, because I and not a lawyer and neither are most people here, the general line is that you cannot 'borrow' directly anything from the universe of their story -- You cannot borrow their nouns (people, places, and things) either in name or in image. You cannot build your story into or around their plot-lines.
You're not dealing with patents here, because gameplay and artistic works aren't patentable. Patents are for machines and processes. You're dealing with two categories of IP protection: copyright and trademark. Copyright protects the originator of the IP from having their work counterfitted, in other words, you can't print up a bunch of Naruto manga and start selling them yourself. Trademark protects the originator of the IP from identity fraud, in other words, you cannot pass of your own work as related to theirs, use the names or likenesses of their creations, or even strongly imply a direct relationship between your otherwise independent work and theirs. Copyright is very concrete, you cannot reproduce in whole or in part, anything created by someone else, even to give it away (educational and other such exemptions notwithstanding). Trademark is intentionally fuzzy, the lay explanation of the rule is essentially that you cannot infringe directly (you can't print your own original Naruto image on a Tshirt and sell it), and you cannot get around this by changing their design "just enough" -- basically, if an average person (mind you, not an average naruto fan, I mean your uncle who's never seen an anime or manga in his life) would confuse your "original" work to be associated with Naruto's trademark, you would be in violation. Similar to copyright, trademark has some exemptions, such as parody or reporting.
All of these rules apply regardless of whether you make money from your work or give it away, and whether or not someone else's work has gotten away with similar -- or even more blatant -- infringement doesn't matter either.
Now, they cannot copyright or trademark general appearances, or general terms. If Naruto has a "Wolf Clan" it doesn't mean you can't also have a "Wolf Clan" (but it probably does mean you can't have your Wolf Clan dress in very a similar manner). You can make a work who's art style is similar, even, though you have to be careful that too many "coincidental" similarities don't add up. At the end of the day, trademark infringement is a little hard to pin down, but its a bit like what someone once said about pornography "I can't tell you what it is, but I know it when I see it."
Also keep in mind that the barrier for legal action, at least in the US, is very, very low. Anyone can initiate legal proceedings against anyone as long as they have standing to do so, for whatever semi-plausible reason. As a defendant, you could then ask the court to summarily dismiss the case, but even hiring a lawyer for just that much can be very expensive.
At the end of the day, you'll be much better off to take inspiration from Naruto, and nothing more.