If it's your system, then you are the admin, and you should be able to deal with them.
If you're not the admin, then you need to speak to your admins to find out why they're allowing other accesses like this.
Either way, if you want our help (as people who are end users), you'll need to explain the probelm in more detail. What "3rd party app"? What do you mean "taken over"? Who is doing it and why do you let them have access? What do you mean by "rewriting"?
So this has nothing to do with the Atlassian Tools.
This is a user community for people who use the Atlassian toolset (http://www.atlassian.com) not for phone related problems.
I would advise you to go the a telecom shop and let them have a look at your phone.
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