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Depends on what kind of alarm system was used - aftermarket, OEM (port or dealership installed), or a custom dealership installed variant. From the way the dealership acted, could be an OEM system - though you'd have to look for yourself to be sure.
Sometimes cutting out the alarm "brain" without removing the inline additions can cause all sorts of problems down the road - like when the battery is disconnected, drains down or if the car needed to be jumped.
If it is the OEM installed one (port-side / dealership installed) - could be as simple as following the wiring harness from the alarm box to the main harness under the dash. Many of the port-side and dealership installed ones used jumper blocks - just disconnect those, reconnect the original connection and you're good to go - no cutting, no splicing. Just look for the box labeled Toyota and/or RS3000 or RS3200 VIP alarm system.
If it is a custom job - unless you know who installed it and how - could be a real nightmare on your hand.
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2002 Corolla S, 1.8L 1ZZ-FE VVT-i
2003 Matrix XRS, 1.8L 2ZZ-GE, VVTL-i (RIP)
2009 Matrix XRS, 2.4L 2AZ-FE VVT-i
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