There aren't many thoughts going through his head at the moment. The only thing he really thinks is that he doesn't want Theseus to get hurt. It doesn't even really occur to him what he does.

One moment, Newt is running towards Theseus. The next moment, Newt has forgo the whole running aspect and just teleports himself between Theseus and the mole. For a moment, he doesn't even register the pain that goes across his back (maybe it's the adrenaline). He just wraps his arms around the other to shield Theseus from the appendages from the infected mole.

He just offers this shaky smile to Theseus.