How to resolve post-update display issues in a Dynamics 365 organization

We recently performed an update on our Microsoft Dynamics 365 organization, and once it was done, I encountered a very peculiar issue.

When I logged into the Dynamics 365 instance, I was greeted with a tab which looked like this:

The Organization loaded in the new window which popped up and in the tab on which it was supposed to come, a message which looked like above, came up. 

This was an issue. 

First of all, it was annoying that the Organization loaded in the new window. Secondly, I was not able to open a different section of the Dynamics 365 instance.

For example, if I wanted to go to the Administration section of my Organization, I kept landing on the App Page.

To go to the Administration Page, first I have to click on Settings/Advanced Settings:

Once I click on that, I should be presented with the Administration Page mode. Instead, I was presented with the App Page.

The URL had an “isappmoderedirect=true” embedded in the URL. I tried changing the property to false and, unfortunately, I couldn’t. 

The Organization was opened in “Application Mode” because of this property in the URL.

What is Application Mode?