As far as I know, EMP works by inducing high voltage currents in electronics, permanently frying any integrated circuitry not shielded by a Faraday cage. Which the K-9 may or may not have. It's not so rare; Your cell phone has that kind of shielding, to keep out interference from--for example--your microwave. And Titan probably has a lot of ambient electromagnetic radiation, so K-9 may have been built with shielding. The shielding in your cell phone wouldn't be strong enough to help against an EMP, though, and it's a toss up as to whether K-9's would have any effect.
But anyway, the classic way to get an EMP is to get a big explosion (nuclear, usually) and let the Earth's electromagnetic field freak out and do the work for you. But (IIRC) the explosion has to take place very high in the atmosphere, so that the air particles have time to do their thing. So in close quarters like HQ, the canon character would have more success just setting up a fluctuating magnetic field, which he/she could probably jury rig a device to do from spare parts in the DSAT, if he/she knew how to do so. (Something possibly involving either a microwave/something that emits microwaves, or a fusion generator of some kind. I couldn't tell you the specifics.) Lightning strikes also generate EMPs; one fried my computer once. And that strong of an electromagnetic field can be really painful if it's very local or directed. It'd probably make anyone in the area throw up from vertigo, at least.
But this seems more promising to me: If you get a light one--not an electromagnetic pulse, but a strong electromagnetic field--probably all it'd do is make his circuits temporarily freak out and wipe his hard drive. See the Supernatural episode Ghostfacers for an example: Dean jury rigs a big electromagnet--I think from a car battery, but I don't remember--sticks it in a duffel bag and sets it on a timer so that a few minutes after they leave, it goes off and wipes all the hard drives in the area. :D If something like that was used against your K-9, it would probably wipe his programming, but not affect his circuits. (That's assuming he's not shielded, because if he is it may not have any effect, depending on the strength of the shielding.) If he's anything like normal computers, he might have limited function from the BIOS, which is programmed directly into the circuitry. Either way, he'd be quite thoroughly incapacitated, but easily recoverable so long as somebody had a backup of his programming. (If not, or if the backup was incomplete, you could have some fun with the followup of him acting really weird and buggy as they tried to fine-tune his programming.)