Please clarify your scenario by an example and what you already got in place.
You got a web site (or idea) backed by dynamic data rather than displaying static pages. You would do that by any means that allows for execution at the server side (php, node.js, asp,jsp), connected to a separate storage system (mysql database) or intermediate higher level web services "API".
Then your objective is to turn that data into output supported by InDesign - (a PDF for delivery to the user of the website or to your own printer, other image formats, but could also be the mentioned "publish online").
The same way that your server side php/asp/jsp connects to its storage engine, it must also connect to InDesign.
For the beginning, let's say there is a strictly local web site on the machine of an "operator" that does not know to handle InDesign, on the same machine licensed for the operator. All they know is to open their browser window, click that "localhost" bookmark and press the button "print" on your web page.
This sends a http request to the local web server (e.g. php), which pulls the matching data from its database.
It then stores the data in an intermediate file, and launches a script on InDesign.
The script opens an InDesign template file, fills in the data from the intermediate file (by means of place, import or reading the file itself) and produces the output file (another intermediate file) or sends it straight to the printer. The script run ends and yields the result (e.g. file name of the output file) to your web server for final delivery.
How the web server (php) accesses InDesign differs on your choice of operating system. To them it is an external program at the command line. On the Mac you can use the osascript command to launch an AppleScript to tell InDesign to run whatever actual script we had above. On Windows it could be powershell or others using COM.
Above "operator" is also your developer environment. You maintain the local web site, edit InDesign templates, run scripts.
Scaling to a fancy big web site open to the world, or just to your corporate intranet, supporting hundreds of users in parallel instead of that single operator user, you will need multiple instances of InDesign. InDesign Server is made for this, and it also solves the problem that the web site users are not individually licensed to use InDesign – at a higher price tag. InDesign Server itself also is accessible via AppleScript or COM, but it adds a web protocol "SOAP" - basically again HTTP plus some XML data, so that the web server can bypass the external program call, and talk to separate machines. You may add a load balancer as intermediary to address the multiple InDesign Server instances, or restart them on failure. The principle remains the same – a script opens a template or creates a blank document, fills in the data and delivers the output.
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