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How to implement IIS authentication in an asp.net web api project?

I've been tasked with enabling authentication and authorization for our project's api. The main goal is to protect the methods from misuse, however we also need to enable a developer from another company to call the methods in their code.
Being new to authentication and authorization I'm overwhelmed with the many different options available for .NET etc. Some techniques look promising until you read that they pass credentials in plain text (basic auth?) or have other issues etc... I'm just looking for a reliable and safe approach.
I'm using IIS to host the web api, and I have seen that one such option is to authenticate at the 'host level'. My supervisor has mentioned this is the preferred approach.
I have looked at many threads and videos regarding authenticating in IIS. From what I can work out, such a solution alerts the user that a certain action requires authentication and to enter their credentials.
My issues are as follows:
Given the other developer is not a member of our domain, how can they authenticate using their (windows?) credentials. Is there an alternative to windows authentication?
How will requiring authorization on certain api actions impact the function of the site normally? I.e. will I have to pass valid credentials to the api in my code, for each request?
Overall I'm just a bit uncertain on how this all works and I appreciate any advice given.

Password protected page

I would like to add a password protected page to my WPF modernUI application and could use some help with it.
First of all I don't really have a clue how to handle this stuff correctly in my case.
My application is used on several machines. The protected page should be some kind of admin-page to edit a database that is used by the app.
My idea is, that there is only one Admin-account. But this account can be used from any machine. The admin should be able to change his password. So there must be some kind of encrypted password file on the server which can be accessed from any machine. I don't want to store the password within the application, as this would mean that the admin has to change his password on every machine.
So my question is: What is the best/safest solution for my idea? I'm just looking for hints as I don't have a clue what to search for.

The best Practise nowadays for distributed client applications who share a Database is indeed not to have direct access to the Database.
What you need is a WebService. A web service can be anything. It just has to be hosted somewhere. It can be an ASP.NET application, a WCF Service, or even something not .NET related like a PHP or Java application.
The communication between your application and your WebService depends on what you decide to use. Today a lot of people are using so called REST APIs which use either XML or JSON as data transfer format and use the HTTP protocol.
Its not hard to implement such an API since there are ton of Libs and Solutions out there.
You could use RestSharp for the communication at your client side. Which is straight forward and simple. You could also consume a WCF Service. Which is hosted in IIS somewhere.
However your Problem is nothing special and there are several solutions available. The decision is on your side since it depends on a lot of things such budget, available infrastructe etc.

Your question is quite broad but as far as WPF is concerned you could implement custom authentication and authorization in your application by creating classes that derive from the IIdentity and IPrincipal interfaces and overriding the application thread’s default identity. Please refer to the following blog post for more information an an example.
Custom authorization in WPF: https://blog.magnusmontin.net/2013/03/24/custom-authorization-in-wpf/
The actual credentials should be stored on some remote server that may be accessed through a web service, WCF service or some other kind of API. The details of how to actually get the credentails would be implemented in the AuthenticationService class in the sample code from the above link.

How to force third party service respect the security?

I have to come up with an integration process to allow existing system to use external data providers. The system is a medical timetable web site, using ASP.NET MVC, that allows the patients to schedule their appointments to doctors.
As far as I go you can see on a figure below:
All the providers must expose my contract ISuperIntegration which will be develop by me. I won't be developing External service 1 and External service 2, they will be developed by other companies.
Here the issue comes: basing on the concept of that I could require the way providers should setup their services to communicate with my website properly, I want to forbid for another third party clients consume "External Service 1" and "External Service 2", Or at least make it difficult to do that.
Here is a list of stuff I am setting:
ISuperIntegration interface. It contains operations related to my domain such as GetSchedule, GetDoctors and so on.
Transport protocol. I don't want it to be complicated so I'm thinking about using HTTP.
And could define some general recommendations but they could be easily avoided.
At the moment I'm thinking of using HTTPS with certificate authentication. It would require the implementer to setup their infrastructure so my web site could properly consume the data.
If I would go with basic HTTP, the implementer would just leave their service to be easily consumed by anyone else, which I don't want.
I hope my question is clear. Will be happy to give any other explanations you want.
I'll really appreciate any your responses, commits. Thank you!

I'd always use HTTPS for things like this. Let's just say that's the cost of doing business. You simply cannot have anyone with a sniffer grab that kind of traffic out of the sky. There's a reason why all banking etc. use HTTPS for things that should be secure.
Apart from that, web services have pretty standard mechanisms for security, I'd recommend looking at OAuth over HTTPS. There are plenty of implementations for that.
If your talking about basic web sites, I'd use a standard security mechanism as well like group based security (which boils down to a username + password). Again, there are plenty of implementations for that.
Basically my main word of advice is: don't go inventing stuff when it comes to security. If you're not an expert, you're probably going to get it wrong, and end up with something that can be intercepted by a third party or (much) worse.

You have several options:
Basic authentication over HTTP.
PRO. Easy to implemet
CON. UserCredentials was going in clear text throuh the network
Implement WS-Security with WCF. For example, they can sign their requests.
PRO. Easy to implement with WCF
CON. Java clients can faced with problems
You can force clients to use HTTPS.
CON. You should setup your web server.

You are like Oracle, they want people to develop in Java language but they also want to forbid competitors to run the Java compiled code on non Oracle's virtual machines, or at least make it difficult to do that :)
So you can do the same by protecting your interface with patent or copyright law. However, I doubt that it is patentable or copyrightable :)

Considering the privacy sensitivity of the data, IMHO it must be encrypted while in transport. Hence HTTPS not HTTP.
Authentication of your service to those providing services to you: well essentially it's up to them, not up to you who they expose it to, similarly how they want it protected is their call. Now assuming you do have a way to make them do the right thing...
Client certificates aren't that expensive nor prohibitive in setup to get up and running. But you do need to register the client certificate (every time it is renewed!) with the server in order to get the needed authorisation (just recognizing it's a valid cert isn't enough: anybody can apply for a (validly signed) certificate ...) .
But all that is relatively painless and rather well documented around the web, and it can be done on almost any platform of choice.

As several people mentioned these earlier you can't guarantee that those external companies will expose your service with specific security settings, it's up to them.
If you are responsible for developing MVC application and WCF service you can only force someone to use specific security settings on the layer between your WCF services and those External 1 and 2 providers.
Btw, here is a good tutorial that can be useful if you want to improve your knowledge about how to configure WCF security.
How External Services expose your service it's up to them. Just image that this is normal web 'proxy' behavior.
Maybe the architecture which your company adopted it is not the best for this solution

Secure connection using SOAP

I need to call a .NET SOAP webservice in a secure way. It must be secure in such a way that others can't call the WebService methods, and also it should not be possible for "the middle man" to understand the content of the messages.
The caller will also be a .NET webapplication installed on another IIS.
I can design the webservice methods as I want, so no restrictions there.
I have been researching HTTPS/SSL with certificates, but I don't know if it actually solves my problems in a good way? For example, it would be anoying if the certificates has an expiration date, although it's not a showstopper in any way.
So how would I go about this in a good way..?
Thanks for any help.

As #BrokenGlass said, SSL only encrypts the traffic between points. It doesn't handle securing individual functions from usage without authorization. Here is a good article on just such a topic using SOAP headers:
How to: Perform Custom Authentication Using SOAP Headers
This can be mixed with any form of authentication except Windows Integrated. To use Windows authentication, you'll need to have a separate library which accesses the Active Directory through the DirectoryServices namespace.

Assuming you control the infrastructure then keeping the server that is providing the web services behind a firewall so it's accessible only from the web servers and implementing IPSec should provide the necessary security.
From the software point of view, this article contains all you need to know about protecting the service interactions.

HTTPS/SSL works fine. Just make sure to renew your certificate in time to avoid warnings and messages for your client.

I need to call a .NET SOAP webservice in
a secure way. It must be secure in
such a way that others can't call the
WebService methods, and also it should
not be possible for "the middle man"
to understand the content of the
messages.
HTTPS/SSL only solves the "middle man" part of what you want to achieve. You would still need proper authentication in place on your web service. You could do this i.e by using the built in Forms authentication and providing a Login method that returns your authentication ticket.

Using OpenID with a WebService: Best way to authenticate?

I'm looking for some guidance on the best way to authenticate to my WebService. Right now, I have a standard WebService on .NET 3.5, and a MVC website that sits on top of this WebService.
The MVC website uses OpenID to authenticate users, and during the development phase, we have simply been passing the user's OpenID Claimed Identifier to the WebService to authenticate. Obviously this is not what we will be releasing to the customer when we go live.
So my question is this: What's the best way to authenticate to the WebService?
Some of the API's I've played around with use Authentication Tokens. Another idea we had was to, upon connection to the WebService, pass the client an encryption key which they could use for all transfers.
I'm thinking out loud here, and again, any help is greatly appreciated! Thanks!
...
UPDATE: Right now I have created a custom SoapAuthenticationHeader which has an OpenIdURL property. This is used on all service calls to authenticate the user. The problem is two-fold:
If a hacker know's a user's OpenIdURL, they can easily gain access to the WebService.
The OpenIdURL is currently passed in plain-text.
So I could pass an encryption key to the client upon connection to the WebService, and have the client encrypt the OpenIdURL in the SoapAuthentication header. But I'm not sure about how to best go about that...

You might want to take a look at OAuth:
http://oauth.net/
(Use http://oauth.net/code/ for coding.)
As it is geared specifically for this scenario (Open ID isn't, really).
There is another question on SA which asks about the best way to secure a web service, and Open ID and OAuth are both discussed:
Web Service Authentication using OpenID

ASMX web services (which Microsoft now considers to be "legacy") have no ability to use OpenID for authentication. They can only use what IIS provides to them. You could possibly add a SoapExtension that would do OpenID authentication for them, but I wouldn't spend time there.
I don't know enough about OpenID to be certain, but I suspect it can integrate with WCF through federated security. I'm sure someone else will answer with details on that.

This isn't really an answer, but I can't leave comments...
You say "I have a standard WebService on .NET 3.5, and a MVC website that sits on top of this WebService".
I might be way off base here, but the language implies that these two sit on the same server. If so, why can't you just share the users database and the cookie token?
James