Board Thread:Questions and Answers/@comment-32272607-20170724171019/@comment-30109283-20170725013947

No. If Malware retains the natural ability to possess any technology, he will only control the Omnitrix, not the person that was wielding it. Now, if Malware is part Ectonurite, then yes, he can possess both Ben and the Omnitrix at the same time.