Let's say you have an app A and B and the user needs to login from A to B. App A consumes a webservice of B that user X wants a token. App B checks if user X exists and then creates a token, attach that one to user X and returns through the webservice this token from app B to A. Now A creates a deeplink with the token as parameter. App B receives the incoming link and retrieves the user belonging to this token and then does the autologin javascript.
Read the documentation of the deeplink. All deeplink have an URL like https://yourapp.mendix.com/link/nameofdeeplink
Nameofdeeplink is the name you attached when setting up the deeplink.
Regards,
Ronald
[EDIT]
The deeplink microflow (microflow with Token as parameter) should create the AutologinHelper object with entities loginToken and URL. The URL can be retrieved with GetApplicationURL from community commons. Then the microflow opens a popup. In the popup put the AutoLoginHelper as page parameter and put the Javascript snippet inside the AutoLoginHelper object.