aftermarket alarm with broken oem alarm

I have a convertible which had a leak during a bad storm (sitting water inside the car) and caused some damage to the wiring throughout the car. I already had to replace the stereo and speakers since they are fried. In addition, constant 12v to the car is nonexistent unless the car is on (I assume the constant 12v wire was shorted/damaged). I either plan to try and find the factory point where that comes through the firewall and fix it, or just run a new wire straight from the battery. My keyless doesn't work at all, even with the car running so I am assuming the module was damaged by the water. I plan to get an aftermarket keyless, remote start, and security systems. My OEM alarm does not work, whether that's because that module was also fried or simply because it has no power to it, I am not sure. Lets say the alarm is broken completely, where it would have to be replaced if I wanted it to function again. Would the aftermarket system act as a an alarm or does it need to function along side the OEM alarm? My hopes were to basically bypass the broken components, get back a keyless entry function, and also add remote start and security in the process. Any help is appreciated.

What make vehicle?

Mitsubishi, Eclipse Spyder

This job is going to be ridiculously expensive. I just threw away a year 2000 Gallant because the engine management had failed = $1000 alone. You're on a hiding to nothing. You can replace ALL the wiring it's quicker than sorting out individual corrosion, fuse blows etc. but you've still got all the processors = $$$$ just to test them; frankly the vehicle's a write off.

What do you mean? The car runs fine. Power windows still work, door locks work (not with key fob, the buttons on the door), air bags are fine, ABS is fine. The only thing I lost was the stereo (the OEM amp was under the seat and fried everything), and things like the interior lights don't turn on which I don't care about. The problem is just that there is no power to accessories with the key out of the ignition, which is what a security system needs, but getting a constant 12v into the interior is easy. I just wanted to know if the factory alarm needs to function in order for an aftermarket alarm to function. If it doesn't, I can just get an after market one installed. If the factory one does need to work then I have to get it fixed first.

Check your main power lead going to the fuse box, it will be the thickest wire, probably white. Same with the under hood fuse box. The answer to your other question is YES; you should be able to add an alarm whether or not the factory unit works. PM me with your email address and it's year, I'll send you the DEI alarm sheet for it.