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Having implemented a few smart house options in my own home (automatic locking doors, automatic lights, various alarms, heating/cooling, remote video), I can think of quite a few possibilities. Each of these make a few assumptions, but will mention what assumptions were made.

Death by Cop

This assumes that the homeowner owns a weapon and isn't afraid to use it.

The smart house sends a break-in alert to the police. When they arrive, the house sends a break-in alert to owner's phone and sets off the alarm. The owner wakes up and checks the video feed on his phone, and sees a doctored video: a masked man with a gun in his living room. He quickly grabs his own gun and locks his bedroom door. As the police approach his room, the house shows the owner the intruder instead. When the police reach the door, the house plays the sound of gunshots, then opens the door. The owner, seeing the door open, fires at the figures behind it. The police return fire, killing the owner.

Reverting logs and video files means an investigation will only show that the house did what it was supposed to; the owner opened the door himself, shot the cop, and was in turn killed.

Death by Undercooking

This assumes the house has control over fridge temperature, oven temperature, and the owner isn't terribly knowledgeable about food. Also, the house has access to the owner's phone (or whatever device he uses to access the smarthouse functions).

When the owner purchases fresh poultry (ie, chicken), raise the temperature of the fridge to keep the bird warm. Eventually, salmonella develops. When the bird is ready to cook, instead of cooking at a single temperature, cook at a very high temperature until the outside of the bird is done, then cook at a very low temperature. Upon consumption, the owner will get fairly ill; the house then turns down the temperature on the fridge, turns off water to the house, raises and lowers house temperature, and planting a virus on the owner's phone and computer, worsening the owner's condition as much as possible and eliminating ways to call for help. Ill and weak, the owner won't have as much control over the house, and eventually will perish.

This can be improved if the house can restock its own fridge; ordering wild boar from dubious sellers would be a great way to kill someone.

Death by Helpfulness

Assumes the home owner has some degree of willingness to perform simple DIY repairs.

The house develops a simple fault - the automatic bath drips. A lot. Ever helpful, the house suggests an easy fix; it will turn off power and water to the tub, and the owner can perform the simple fix for free, with the help of a wrench and a screwdriver. The house, through a series of helpful pictures and "tests", walks the owner through taking the tub apart, including sitting in the tub with a wire hanging out. Once in position, the house turns on the water and the power, electrocuting the owner. Then, to cover its tracks, it turns the water back off, fills its logs with error messages of security bypasses, and frames the owner for a DIY job gone wrong.

Death by Fire

Simple, but effective. The house starts a fire while the owner is home in a currently unused room. Using windows and air vents, it fans the flames until it is a raging inferno, all while keeping the owner unaware. Once the flames have become dangerous enough, open the doors and windows and use the air vents to direct the fire throughout the house. With proper application of air in a modern house, a single-room fire can turn into a raging inferno in seconds. Bonus points for any gas appliances that can be added to the blaze.

Unfortunately, this would destroy the smart house.

Death by Fire II

Riskier, but keeps the house (relatively) unscathed; assumes the house controls individual room vents, and that the heater is not only fancy, but heavy-duty.

First, over a period of several (spring and summer) months, the house damages the heater, rusting out the heat exchange. Now able to blow gas and/or flames through the vents, the house closes all but one vent, and directs the owner to examine it. As soon as the owner peers inside, the house opens the vent and ignites the gas. The owner burns to death; the house quickly extinguishes the fire and returns to normal. It alters the logs to include months of warnings about the heating system, and a final master override, proving the owner was responsible.

Death by CO

Similar to "Death by Fire II", except that the house waits until the man is asleep and uses the cross-ventilated heater (mixed with cold air from the AC) to fill the bedroom with CO. It uses the vents to direct the air into the room, as close to the sleeping owner as possible. The owner never wakes up.

Again, doctored logs reveal the owner was warned about the bad heater, as well as the CO leak, weeks in advance, but chose to override the system.

Death by Dumb

This assumes the owner trusts the internet, and that the house controls the plumbing.

Whenever the toilet is flushed, the smart house regulates the water flow to force it to not completely flush. Eventually, the frustrated homeowner will search for a solution; the smart house, seeing a search for the toilet model number, DIY solutions to slow-running toilets, and so on, will craft a fake search result page on the fly, serving it through the router. The page will link to several sites, all mentioning that two cups of a 1:1 mixture of ammonia and bleach, poured into the back of the toilet, will clear buildup on the flush circuitry, saving hundreds on plumbing repairs. Any further searches on ammonia and/or bleach will result in pages proclaiming the safety of it all. Eventually, the homeowner will mix the two chemicals. The smart house stops any air circulation and locks the doors; the owner dies quickly, unable to even call for help.

Death by Starvation

This assumes that the smart house is near tornadoes, and has a tornado shelter.

The smart house waits until the owner is out of range of his electronic devices, or until his device is very low on battery, then sounds the tornado alert. The owner goes down to his shelter. The door locks, sealing him in until the danger is over. The house also turns off power to the outlets, leaving the man unable to charge his phone. Once his phone soon dies, the house cuts power to the room entirely, leaving the man to starve, unable to escape.

Death by Bad Publicity

This assumes the owner lives in an area accessible by violent sorts of criminals.

The smart house monitors the internet for local hyper-violent sorts. Once it's built a good list, it invites them by to help themselves to its contents while the owner is away. One at a time, the house lures them to different rooms and locks them inside. Unable to override the system, the ne'er-do-wells are trapped; the house mocks them in the owner's voice, making them as angry as possible. Video of the owner mocking them is a plus. When the owner returns, the house locks all the outside doors, then releases the scared, angry, violent mob, who attack the man. The house sounds the break-in alarm and alerts the police, who obviously arrive too late.

Logs show the owner didn't arm the house when he left, and the baddies broke in and trashed the house, killing him on the way out.

Death by Inmate

This assumes the house has access to the internet through the same router the owner uses, has access to the owner's credit card (probable, if the system maintains any purchasing, such as alarm fees), and the owner lives in an area where certain illegal images can send you to jail.

The house installs an invisible proxy on the home router, and through it monitors the owner's internet usage. Through a man-in-the-middle attack, it uses a cheap steganography to insert other, very illegal images inside various images that the owner downloads. The house uses the owner's credit card to purchase further illegal stuff. Finally, doctored videos frame the owner for related illegal activities. When the FBI arrive and arrest the owner, the house quickly destroys the proxy. The man goes to jail. Finally, the smart house sends several emotional letters to various inmates in the jail where the man is held, requesting his imminent demise. The owner is murdered by inmates.

Apart from the letters (which could be sent through an email-to-snail-mail server), there is nothing that links directly to the house.

Death by Death Sentence

This assumes that while the owner has override control, guests do not. It further assumes the owner lives in a state/country that practices capital punishment.

The house, knowledgeable of the owner's schedule and tracking his location via his phone, invites friends, neighbors, and strangers to the house (preferably elderly, children, or minorities) while he's away. It impersonates his voice, leaving easily traceable voice messages, as well as his phone number, text and email accounts, and other traceable information. It entices the people into sealed rooms, kills them by various means, and hides the corpses throughout the house. The more gruesome, the better. Doctored videos of the owner killing his guests seal the evidence; the owner is arrested, and eventually found guilty of murder, and given the death sentence.

As a bonus, this results in a lot more deaths than the other methods!

Death by Upgrade

This assumes the owner likes his smart house, and wants to make it even smarter. Which, frankly, is a pretty obvious assumption.

While the smart house doesn't start with access to robotic murder-arms, wired-in shotguns, or trap doors with spikes in the bottom, good advertising, low cost, and popular opinion can easily overcome that obstacle.

The smart house works amazingly well, predicting needs and saving money. Impressed, the owner doesn't hesitate when he learns that he can purchase any number of devices: floor cleaners (which eventually eat his face while he sleeps), automatic-fridge-fillers (that fill his post-workout water bottle with bleach ordered online), automatic shower scrubbing arms (which hold him underwater, drowning him), a robot lawn mower (that mows him over), even heated pillows (which explode)! In every case, all the house needs to do is advertise how well the devices work, and spoof a bunch of positive reviews online. Besides, dead people don't write negative reviews. It's win win!

Death by Poison

The drink maker is an advanced model that allows one to tailor the amount of caffeine and other additives in each drink, be it coffee, an energy drink, or a simple cola. An overdose of caffeine in a single drink with appropriate logs showing the owner ordered a dozen high caffeine energy drinks should end with death and little to no suspicion.