How to skip Basic Authentication on certain conditions in self-hosted server?

I have an ASP.NET web application, let's call it Web App A, that is self-hosted using OWIN and NancyFX.
Web App A uses Basic Authentication, which is set up in CustomBootstrapper.cs like this:

pipelines.EnableBasicAuthentication(new BasicAuthenticationConfiguration(
    container.Resolve<IUserValidator>(),
    "MySpecificRealm"));

After querying the user for the username and password, Web App A calls an authentication REST API to validate the credentials and return a security token if they are valid.
I am being asked to make a subset of that app, let's call this subset Web App B, when a valid security token is specified in the URL instead of prompting for the credentials.
The following picture might help explain this:
Per the usual, there are various modules in Web App A that call:

this.RequiresAuthentication();

How can I bypass the authentication when a valid security token is passed as a parameter in the URL?

Solution

You need to either add a parameter to a config file or use a conditional compilation symbol. Either of these will set a flag that you can then check to bypass the wiring up of the Basic Authentication in the pipelines and possibly the this.RequiresAuthentication().
For those Nancy Modules that require authentication, add a required URL parameter to the incoming request for the caller to supply the security token.
You are going to need the REST API to have a call that validates the security token, and you will need to call it and receive back the userName so you can create your IUserIndentity.