Ions are here probably multiple ionized nuclei of heavy, but not too heavy nuclei. That is because they are strongly charged, thus they can be accelerated efficiently.
Ion cannon is probably some type of VASIMR (see on wiki), which is an electromagnetic resonator (like mocrowave oven) which accelerates charged particles by EM waves no nearly speed of light.
About "phasing": quantummechanical systems are described by a wave function, which has complex values. These complex values have phase. Phase is not directly observable, but has an indirect role when this qm system interacts.
Phasing could be some type of quantummechanical coherence between the target and the phase of these charged ions. Likely its goal is to make the charged ion bombing more efficient.