I was a little surprised at the last line in your code:

window.jQuery.prototype.marginotes = window.$.prototype.marginotes = marginotes

Last I checked (one minute ago) jQuery and $ refer to the same object. jQuery === $ unless somebody is using $ to refer to something else in which case thanks you just clobbered $'s prototype. You should follow the jQuery conventions https://learn.jquery.com/plugins/basic-plugin-creation/

For example, we can achieve an effect similar to the one shown here using just CSS (no JS) if we’re able to use position:relative on the containing paragraph without breaking anything else in the styling:

HTML:

    <p class="note-container">This is some text with a <span class="note" desc="Style me!">marginal note</span>. Lorem ipsum dolor sit amet...</p>

    .note-container {
      position: relative;
      width: 400px;
    }
    
    .note {
      text-decoration: underline;
    }
    
    .note:hover::after {
      content: attr(desc);
      position: absolute;
      top: 0;
      left: 440px;
      width: 150px;
      height: 100%;
      border-left: 1px solid black;
      padding-left: 9px;
    }

https://jsfiddle.net/2ejk2who/

However, what happens if we need to work with touch-only devices, where hover effects aren’t available? Two options would be to show the notes all the time, or to embed a hidden checkbox and make the anchor text its label. In the latter case, tapping on the text could then toggle whether the marginal note appears if we used something based on :checked instead of :hover.

But now what if more than one note is set to visible at once? We can’t combine the position:absolute technique to get neat alignment at the top of the paragraph with using floats so multiple notes automatically fall under one another. I don’t have a good pure-CSS answer for this one.

In any case, on a smaller screen we might not want to show marginal notes alongside the main text anyway. It would be helpful if there were a way to have the notes drop underneath the paragraph and stack up, but again, we can’t combine the kind of absolute positioning that would place a note there with something that extends the paragraph’s box so later content moves down after any visible notes.

Perhaps one day we’ll have more flexible options for generated content and CSS positioning that will let us do these things, but for now the only ways I know to achieve some of these effects still rely on JS.

Edit: There were two gotchas beyond browser compatibility. jQuery provides a consistent interface to set numeric style values - in vanilla Javascript you have to remember to turn these numbers into strings suffixed with "px". And I hacked together the code that stops fadein and fadeout from stepping on each other.

Changes: https://github.com/fdansv/marginotes/pull/2 Working Example: http://mshenfield.github.io/fdansv.github.io/

So you can tell us: what happens if you have Javascript turned off?

I have sympathy for the "what happens if I'm using a screen reader or other accessibility device" question, not excluding those who need to use assertive technologies where possible is important. geocar's post below suggests what might be a better implementation in that regard, which will support your use case too, but some advanced screen readers might try run the script (to access generated content like Google does for indexing) and then not read the text because said code has hidden it via DOM manipulation, meaning the technique might not work in all cases.

But disabling all javascript and expecting the world to support your preference in everything we produce (you can at least read be core content in this case) feels a bit entitled IMO, along the lines of people/companies (who I deal with in my day job) who use legacy browsers and are upset when that means they can't have shiny new features in the browser based applications that they use (or want to use).

I understand the desire to block all the iffy JS (adverts, particularly adverts that eat CPU cycles and therefore my battery when mobile, tracking, and so on) and I understand that running noscript or similar plugins is too cumbersome in many opinions, but unless you are paying for the content in some way you can't really expect to demand to control how it is delivered to you.

A thought for reducing tracking and such without blocking code used for page functionality: I'd like to see browsers block 3rd party code as an option (as some do for 3rd party cookies), with a whitelist to enable CDNs (possibly with the major CDNs on the whitelist by default). That would still allow iffy code if it is served from the same site (by design or because it has been hacked) so isn't perfect, but it might be a good compromise.