I was aware that there was something hot pressed against my temples, the electrode feeds of the Compact Animus. The light from the visor was too bright. Even as I closed my eyes the light made the world a fleshy pink nightmare enveloped in the heat and smell of smoking circuitry.

"What the fuck!" protested Helen's voice, then the swoosh of a fire extinguisher. I tore the visor from my eyes and sat up straight. There was a sudden tightness in my head and chest, as I realised I wasn't breathing.

I gulped in a couple of lungfuls of air, the first was fine, clean, relieved all the pressure. The second made me double up choking. The smoke levels weren't lethal but they were enough to rouse prickles of pain in my chest.

"Something happened in the synchronization matrix!" Paul said. "It started to read a confusion between Sam's pattern and Yughi's, then the disc speed ramped up, like the Animus was trying to access too much data all at once. It's okay, everything's under control now."

This was followed by a second loud whoosh of air as Paul blew a thick coating of yellow dust off the blocky shape of the Compact Animus.

"It needs some time to cool down before we can boot it again," Paul said. "Sorry about that people."

"Well I've been pushing it pretty hard," Helen said. "I guess this means it's break time."

I took a shower, made myself some noodles and then asked if I could go out for a walk. Helen told me it was too dangerous, which is how I ended up on the roof terrace, clutching a fresh cup of tea.

Dusk was falling in London, the safe house in Crouch End was on a hill looking down towards the city, where office building lights twinkled in the early evening. I breathed in some smoke-free, smog-filled London air and took a minute to review.

One of the really weird things about spending time in the animus was coming back to reality and being able to tell it apart from the simulation. There was, as far as I could discern, no qualitative difference between feelings in and out of the animus.

But you could still tell what was real and what was a historical replay, somehow.

What made that difference?

The most obvious thing was a level of abstraction when in the animus. In reality, I was me, inside I still felt like me but I was watching reality pass by through Yughi's eyes. There were times when I controlled Yughi, the animus filled in by highlighting waypoints through an augmented reality overlay. Whenever I got into the guts of a memory Yughi spoke, Yughi acted and I was just along for the ride.

Resisting Yughi made me feel giddy and nauseous like I had before I achieved synchronization. That was the most distancing part of the whole experience, the feeling like you were experiencing an incredibly bizarre and vivid flashback to a part of your life that never existed.

As I sat, sipping at my tea, revelling in reality, I began to feel that my time in the animus had changed me at a fundamental level. It was just small things, the way I picked up my cup, the way I held my body as I sat. I had felt fine before going into the animus, now I felt out of shape, I felt like my own body didn't fit, somehow.

I swallowed the rest of the tea and, somewhat out of character, I began to work out. It was a mish-mash of exercise moves I'd learned over my life, squat thrusts, star jumps, stomach crunches, lifts, bounces. Before now getting out of breath, heart thudding, sweat prickling my skin, had felt unpleasant. Now, however, it felt like I had, in some strange way, come home.

While I was doing press-ups Helen came out on the balcony.

"Sorry," she said. "I didn't mean to disturb you."

"It's fine," I said. "Are we ready to reboot."

"That's right," Helen said. "Are you feeling okay?"

"Well, mostly," I replied. "Honestly, I don't really know why I came out here and started working out. I've never really had an urge to before."

"I see," Helen said, she pursed her lips as if she wanted to say more but was holding back. "Let's go and run some diagnostics," she said.

We both went back inside.

"Can you check Sam's neurals," Helen asked Paul. "He says he's experiencing some dissociative drives and motivations."

"That's not exactly what I said," I replied.

"What happened?" Paul asked me.

"I was just..." I said, suddenly self-conscious, pointing back towards the passage to the balcony stairs. "I mean, I was working out. All I said was that I didn't really do that much before, arbitrary exercise. I like to swim, I like to ride my bicycle. Maybe I was just feeling a bit like I hadn't moved in a while."

"Maybe," Paul said. "There is a chance we've got the synchronization assistance buffers slightly over-tuned after earlier. That would explain why the system suddenly crashed. I'd best do some checks. There will be some bleeding effect of motor skills over time, but nothing should have happened this fast."

Something flipped in the pit of my stomach at the mention of a 'bleeding effect', nobody had mentioned this before.

"What are you talking about, what's going to happen to my motor skills?" I asked.

"When I worked for Abstergo..." Paul said. He paused and sighed. "I heard some things from one of the top guy's labs. His name was Dr Warren Vidic, he was spearheading research projects using the animus technology, level one classified. There was never anything official but it seems a couple of the test candidates they... well, they died in the chair."

Registering my look of alarm Paul was quick to flap his hands about. "Oh, this was years ago now," he said. "The technology is completely stable now, plus there's a huge body of work on the relationship between the animus and its host subject."

"Make me feel better about not dying with that black plastic headset on," I said. I could hear a weird kind of flat authority in my tone, that scared me too, I'd never really had a knack for demanding things, suddenly there it was, a demand.

"The neural link into the animus works on a bidirectional synthetic feedback loop," Paul said quickly. "Your brain makes demands of it to achieve synch and, in turn, the animus asks for your brain to conform to the data it's feeding. This means that, inevitably, parts of your ancestor leak through into your brain. It's mostly harmless and that's at worst, it can actually have incredible benefits.

"The bleeding effect will teach you any motor skills your ancestor had. Essentially, if your ancestor was a concert pianist then, with enough exposure, you will become one too.

"The problem is that the neural output of your brain is analogue and the codec to translate that output into terms the animus could work with wasn't always as safe as it is now. Motor skill information will create a tighter better synch with the host but if actual memory and personality stuff breach the wall, as it were well...

"Imagine that your brain is, I don't know, a ball of ice cream wafer. Now imagine that your ancestor's brain is the same. Imagine what would happen if someone or something tried to push both of those wafers into the same space at the same time, both would be destroyed.

"It's vital that all you get is motor skill memory and memory of things like crafting, tracking, basically any learned skill. If parts of Yughi actually try to get into your brain it would be bad. Our software's extremely sophisticated at screening for that but... this is new stuff. I think it would be best just to run some diagnostics."

"Well, there's something I think we can both agree on," I said.

"Sam, don't worry, whatever secrets your DNA holds... we can't get to them if you're dead," Helen said. "Abstergo have no problem in that regard. With a strong genetic sample, they can upload all of that information into their cloud server, have a room of low paid desk jockeys surfing through your ancestor's DNA. They'll plunder it for information in a week or two. They don't need you, they just need your genetic code."

"You know how to make a guy feel special," I said as I relaxed back on the sofa and put the headset on. The visor of the animus was up, the electrodes were in place against my temples but the feedback synchronization band wasn't engaged.

"She's just telling you the truth," Paul said as he pored over a number of bar chart and graph readouts that had appeared the moment I had put on the headset.

"I thought nothing was true," I said.

"You have to trust us," Helen said.

"Why?" I asked.

"Because Abstergo have ensured that you don't have a choice," Helen replied.

"I'm going to run you through a few basic synchronic setup routines I found when I rebooted the system," Paul said. "I think we can tweak the loop so we shouldn't have another synch dump."

"Wouldn't it have been a good idea to know what was in this system before you strapped someone into it?" I asked.

"It would," Helen said. "We only stole this prototype seven hours before we came for you, so time was not on our side. It still isn't," she finished pointedly.

"Okay, fine," I said, I lay back and pulled the visor down. The blackness of the animus base state didn't last long.