SCIENCE determines that reality has a few more dimensions than we previously knew about. Some of them are pretty domestic- a gravity dimension, tachyon dimension, etc- others, not so much.
Not knowing *how* these higher dimensions work doesn't prevent someone from making use of them or experiencing them- for example, we're obviously affected by gravity in spite of us not knowing all the details. It applies to the higher, more magical dimensions.
Your PCs are part of a much bigger organization, which might be part of an even bigger bureau. These special forces soldiers are trained in every conventional form of combat, and are supplemented by magic tech to deal with paranormal threats from higher planes of existence. Specialists include natives (ie, hire a voodoo contractor when taking on Caribbean vampire drug lords), paranormal entities, etc.
A larger plot hook could involve dealings with beings from both higher dimensions and other planets. Think Mi-Go from Lovecraft/Delta Green.