By the sounds of it, your custom theme is missing the common hooks that allow plugins to alter/output their code.
To take a simple example, every theme should have a call to wp_head() somewhere in the section of the output page. This allows a plugin to “hook” into your , and for example, output code to load its Javascript.
Here’s a real-life example. The WordPress Twentyfifteen theme has this in its header.php file (traditionally the part of a theme that outputs the section of any page):
... other <head> stuff
wp_head();
wp_footer();
?>
</head>
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