On the gen 6 the main loom from the ignition barrel to the junction box is where I have seen most immobilisers fitted on gen 6's. If its CAT1 then all the wires from this loom to the immobiliser will be black, however this doesn't really matter. What you are looking for is the 2 wires on the car loom that have been split. Its normally fairly obvious which ones it is once you get access into the loom. Note, you can remove this loom completely, its only about 12" long from what I remember. Once its off the car you will be able to see the loom wires are coloured and you just need to join them back together again.
Once you have these out, the rest of the immobilser wires will be for remote central locking, the wiring to the siren if there is an alarm, wiring to the fob receiver. Probably also live and ground feeds etc. You just need to follow them back and carefully remove them and make sure you insulate any exposed wires.