This is a 1998 Honda Accord EX. Only the ignition key came with the car, no door key. So I leave it unlocked. When I open the door, the headlights flash on and off for 2 minutes and then stop. If I start the car, the headlights again flash for 2 minutes. Only after shutting the car off, a green key light flashes 5 times on the dashboard. When I open the door to exit the vehicle, the headlights flash again for 2 minutes.

I suspect this is an issue with whatever security system Honda included. The previous owner did some janky stuff to this car. So I'm wondering if this is actually the alarm going off and the previous owner just disabled the horn part of the alarm.

I was suspecting the transponder key wasn't programmed (or it doesn't have a chip in the key), but the car starts and runs fine.

Does anyone know what this means when the lights are flashing like that? And how to fix this?

There is also a little red blinky light next to the door lock on the driver's door. That seems to always be blinking. Perhaps the security is always armed? In that case, how do I disarm it?

 

This does sound like an alarm/security issue.

Take a look under the dash around the steering wheel. Look to see if an aftermarket alarm/remote starter system is installed. It would be very obvious, because the installers typically have wires running all over the place. OEM wiring is pretty neat and organized with most of the wires in plastic sheathing.

 

I don't think there is any aftermarket alarm/security installed. I believe this is the OEM security system. As the lights flash, I can hear a relay clicking in sync with them, somewhere in the dash on the passenger side, near the glove compartment.

I haven't pulled the steering column apart, but the center console, radio, and climate control, all have their covers/fascia removed. All the wiring in there looks OEM.

New info: I tested all the fuses (in all 3 fuse boxes) and found 3 blown fuses. I replaced them but no change. One of the 3 blown ones was a 20A in the fuse box under the hood. The instant I touched the replacement fuse to the contacts, the horn beeped, fuse sparked, and it blew immediately. So there is a short or something causing overcurrent on the horn circuit. That will be a separate issue I'll investigate at another time.

This is relevant to the issue at hand, though, because now I know the horn/alarm is being triggered with the lights flashing. I'm just not hearing the horn because that circuit is open due to the blown fuse.

 

You don't have to take apart the steering column. You might have to remove a plastic panel on the bottom and look above the gas and brake pedals. That is typically the location an aftermarket security system is installed.

What are the labels on the fuses that are blown? Did the other two fuses blow when installed new ones?

 

There's no aftermarket wiring or modules. It looks all original. And the relay clicking over on the passenger side, tells me it's most likely OEM (Granted, I do know that an aftermarket could be triggering an OEM relay). I've done aftermarket security systems and remote starters, and they're usually mounted behind the instrument cluster, on the steering column, or somewhere around that area. I don't see any signs of that.

I read the labels on the blown fuses, but I forgot what they were. It was 15° outside so I did it hastily. I may have to wait a bit because it's going to be around 0° the next few days. The other 2 fuses did not immediately blow, but I didn't check them again after starting/running the car. I'll have to do that when I get back out there.

I ordered a fob, which it seems I should be able to program myself. Once I get that, maybe pressing unlock will disarm the alarm (hopefully).

 

These were the blown fuses:
20A labeled STOP in fuse box under the hood. Brake lights and horn. I disconnected the horn and pulled the relay and now the brake lights work and the fuse doesn't blow. Resolved, for now (will need to replace horn).
20A #9 Radio Cigarette Lighter in passenger side fuse box. I replaced the fuse once and it hasn't blown again. Resolved.
10A #10 Small Light License Light in passenger side fuse box. This one still blows immediately, whenever tail lights are turned on. The brake lights do not effect this. Still trying to figure this one out.

The lights flashing are definitely the factory alarm going off. Once I got that fob, I was able to disarm it by pressing unlock. The alarm can only be disarmed by the door key (which I don't have) or the fob. The ignition key, pulling the door lock pin, or pressing the power lock switch on the door does NOT disarm the alarm.

 

For the door key, you can take the door lock cylinders to a locksmith and have them re-pinned for your ignition swich key. You can do this as well. It is obviously not critical, but can be a project in the future.

For the fuse issue.... If that 10A fuse only blows when you turn on the parking lights, then you have to have a short past the taillight relay. When you turn on the parking lights, the relay sends power from that fuse to the parking lights on all four corners of the vehicle plus the license plate lights. It also sends power to the driver's MICU (in driver's fuse box). You can try removing all the parking light bulbs to eliminate a short at the bulb connectors.

Finding a short can be tedious, so maybe start with common areas. One area to inspect is the harness going from the trunk to the trunk lid. That harness flexes when opening/closing the trunk lid and is a prime suspect for broken wires. If your car was ever in an accident, I'd inspect the wire harness plastc sheathing for damage like a hole rubbed through or being pinched. You may want to look behind the passenger fuse box to see if the connector has any corrosion that could short the relay.

I also suggest purchasing the 98-02 shop manual. You can get a pdf from automanualsource.com for ~$22 and is worth every penny for this kind of stuff.

 

I think they'd have to replace the door lock cylinder because the ignition key doesn't seem to fully fit into the lock. Regardless, I'm trying to spend as little as possible on this car because it is so old and beat up. I'm between jobs right now. When I start working again, I'll be buying a newer more reliable car.
I don't think the parking lights are the issue. Although, I've never been able to test them alone because the headlights flash whenever I open the door. Since the headlights flash, the tail lights come on with them and that fuse blows immediately. I believe the parking lights are on that same circuit, so they also do not work.
I did check the trunk harness and didn't see any issues. The previous owner told me he was in an accident. The metal in front of the radiator and behind the front bumper is bent. So the bumper doesn't quite fit. I don't see any relevant wiring there, though. I'll see if I can pull the passenger fuse box out to check behind it.
​​​​​​​I'll consider, but that's more money I don't want to spend right now. I did pick up a used Haynes manual for $10. But the wiring diagrams haven't been helpful.

 

I get not spending money in your current situation.

Are the lights still flashing like the alarm is going off? An earlier post made it sound like your fob fixed the alarm issue. BTW, I'm pretty sure the fob is the only thing that can disable the alarm and not the door key. Your last post makes it sound like the lights are still flashing and causing the fuse to blow.

 

I returned that fob because it was horrible quality, and I couldn't roll the windows down by holding the unlock button. I ordered another one but it seems to be lost in USPS-land somewhere. Tracking shows it bouncing between IN and AZ a couple times. So as of current, the lights still flash whenever I open a door. When I had the fob, the lights didn't flash like this, so it was basically resolved.
However, even with the fob, the lights will still flash once or twice when I press lock/unlock. That is enough to blow the fuse.
I thought I read somewhere that a door key would disarm the alarm, but I can't test this. So you're probably right that only the fob can disarm it.