If [Ni(en)3]cl2 is an octahedral coordination complex with 'en' taking 6 ligands,what happens to the cl2?

Upon complexation of the ethylenediamine (en) ligands, the chloride are displaced from the coordination sphere. Rightly as you state, the nickel(ii) is hexacoordinate: each of these is occupied by one the ammine groups of the en ligand (en is a bidentate ligand - it has two ligand donor groups). Since the EN ligands are neutral, when they complex with the Nickel(ii), overall the complex is dicationic positively charged. Hence to balance to overall charge, the chlorides simply float about in solution, or bound in a solid lattice, UNCOORDINATED to the complex.