The easiest, and automatic, way is to enable output post-processing and add a style rule to intent your paragraphs. Alternatively, you may do it manually, if you'd prefer, or need, to do so.
Automatically
Add the following to your Story JavaScript (Twine 2) or script-tagged passage (all other compilers):
Config.cleanupWikifierOutput = true;
Then add something like the following to your Story Stylesheet (Twine 2) or stylesheet-tagged passage (all other compilers):
.passage>p {
text-indent: 2em;
}
Manually
Within your passages, wrap your paragraphs within <p></p> tags. For example:
<p>Lorem ipsum dolor sit amet, consectetur adipiscing elit.</p>
<p>Vestibulum accumsan dignissim urna eu fermentum.</p>
<p>Curabitur sit amet tempus nisl.</p>
<p>Pellentesque ac tincidunt quam.</p>
<p>In sit amet elit et augue tempor mollis non id risus.</p>
Then add something like the following to your Story Stylesheet (Twine 2) or stylesheet-tagged passage (all other compilers):
.passage>p {
text-indent: 2em;
}