The first time we decided to check out Lower Bay, our crew consisted of myself (Mister Snee [aka flameout, or something]), NFF, Krall, Dain Bramaged, and Asher. We had only read about the abandoned station, and were anxious to see it for ourselves.
Our departure from the Museum platform was without incident -- it was late evening and few people were about. We waited for both trains to leave, opened the gate at the north end of the platform and hurried past the live lines into the disused middle tunnel.
We scurried along a ledge on the right side of the tunnel, next to the electrified third rail, as quickly as we dared to. I found myself wondering if I really had enough clearance to safely press myself up against the wall, should a train need to switch onto this track for some reason. It wasn't a comforting thought.
As we walked down the track, we decided that if a train did come down this track we could simply jump through one of the "windows" into the adjacent live track -- but this proved to be less and less feasible as the track started to descend and the windows got higher and higher until they were out of reach. At that point, we were pretty much committed to pressing up against the wall in an emergency and hoping for the best.
We were a few hundred feet into the tunnel and had just taken a sharp turn when we heard a low rumbling sound. We all froze, hoping it was some nearby machine room, or just our imaginations. Alas, the sound grew louder and stronger, the distant rumbling escalating into a full-fledged, echoing roar, as the walls and floor quaked around us terrifyingly. We cursed, shouted, and exchanged panicked glances as we flattened ourselves against the wall, heads turned, hoping for the best, while the roar came to a deafening crescendo and light filled the tunnel...
Then promptly accelerated off, nowhere near us, into the distance.
A train had been passing in the opposite direction on one of the adjacent live tracks, a good twenty feet above us -- its headlights had been flickering into our tunnel through the high-up windows in the concrete walls.
It was, to put it simply, one hell of a scare.
Shaken and pumped with adrenaline, we quickened our pace through the tunnel. No more than a minute later the other train passed overhead, in the other direction. Five or six trains would shake this tunnel before we made it to the abandoned platform, and it was terrifying every time.
Our ledge would occasionally widen mercifully or narrow precariously, and at one point I felt safer jumping over the third rail and walking on the track than risking stumbling onto it from the narrow ledge. Eventually we came to the tunnel's first real safe spot yet -- a little crevasse in the concrete wall with a fire extinguisher and, I believe, a broom. It was dark and relatively small but it did provide temporary shelter from the desperate inertia of running the track, so it was a welcome rest stop. NFF and I ran up ahead a bit from here to see where the next safe spot was. We couldn't see one, so we just called everyone ahead and went on our way.
We were all rather inexperienced in tunnel-running so we still tended to mildly panic whenever a train rushed by in one of the adjacent active lines, and this happened a few times before we came to our next safe spot -- a small utility area off the side of the tracks.
It had a ladder going up to street level, another ladder going down into the gastrointestinal nightmare that is municipal sanitary, and lots of fun pipes, valves and what-not. We got our bearings here then headed back out onto the tracks and rushed forward until, just around the corner, we caught sight of the gleaming, well-lit and completely empty Lower Bay station.
Gleefully, we climbed the steps to the platform, opened the (seemingly ironic) "DANGER" gate and walked out onto the platform. There was much to see -- parts of escalators, random machinery junk, a fire extinguisher last refilled about a decade ago, and other such marvels of modern living. There was one room in which stood a huge tank -- it resembled a water heater -- which was prominently labeled "WARNING: ASBESTOS INSULATION! DO NOT KICK UP DUST!" I had Asher take a photograph of me with my arm around the tank, beaming like an idiot. It didn't turn out. Bastards.
The room with the tank contained more exciting maintenanceish and utility-esque things, and was connected to the south end of the platform by means of a crawlspace running underneath half the station.
We explored, poked at things, took a bunch of photos (which, I reiterate, did not turn out) and basically acted like children in a candy shop or some similarly trite cliche. We briefly explored the tracks just north of the station, where much junk was stored, and Krall desperately wanted to follow them north a ways, but I opted out of it on account of having no clue whether or not the lines were live. Every few minutes we could hear a train screech into Upper Bay, unload and depart, and it was becoming nerve-wracking.
Once we'd had our fill of Lower Bay, we bid it a fond farewell and prepared ourselves to emerge onto a busy Upper Bay through an unmarked, locked metal door. Acting as if we were leaving a washroom or something appropriately average, we opened the door, strolled out and let it lock behind us. We were covered in subway tunnel grime and a cut I had on my hand was becoming badly infected by it -- but hey, what a goddamn kick.

About a month later we returned to Lower Bay with a slightly smaller crew -- the only people on the actual journey this time were myself, Krall, Dain Bramaged and a guy named Korey. I had Asher's camera with me and was determined to return with some actual photographic evidence this time.
Museum was much busier than it had been when we last ran to Bay, so we spent some time milling about, waiting for enough people to clear off. After we had missed about four trains in each direction we decided we were probably starting to appear suspicious, so we waited for the trains to clear out then hurried into the tunnels while Asher kept an eye out on the platform.
We'd been timing the trains and decided we had somewhere in the area of two minutes to get deep enough into the third track that the driver of either train couldn't see us when they passed -- thus falling into what seems to be a common and fatal error in tunnel-running: depending on the trains to have any sort of goddamned consistency whatsoever. Our departure from Museum must have been poorly-timed, because no sooner had we stepped off the platform than the northbound train (the same direction we were going) pulled into Museum. We had left on the southbound side of the platform, so there were a few concrete wall segments between us and the northbound side. The four of us ran for the nearest one and flattened ourselves against it, so that we couldn't be seen from the northbound tunnel. It chimed and accelerated out of the station, whipping up a tremendous gale around us as it disappeared into the distance. We took stock of the situation briefly and saw no TTC police headed in our direction, so figured the prudent thing would probably be to run the tunnel to Lower Bay, fast. We didn't think the driver had seen us, but if he had, he would probably radio Museum security. We took off.
While we hurried along the ledge, I snapped a few photos, and Krall goofed around in general, secure in his experience of having been here and not died before. It wasn't long before we heard the familiar rumbling around us -- earlier, we had agreed that we would all act terrified when this came up, for Korey's benefit. Or something.
Krall and I looked at each other and I shouted "shit, they must be running a train in the tunnel today!" We pressed ourselves against the wall as the train whipped by overhead. We looked like fools, but frankly it was worth it to see the look of abject terror, or perhaps quiet disbelief, on Korey's face. Who knows.
So we went on our way, snapped more photos, did our thing and got to Lower Bay without incident. Some things had changed -- they had locked the room with the asbestos tank, meaning I couldn't re-shoot what I was sure would have been my favourite picture (it occurred to me later that I could have got into the room through the crawlspace under the station -- ah, hindsight), and some old movie props had been moved around. Other than that, it was the same old station. We went to its north end again, and this time Krall made it clear that he was determined to explore further up these tunnels. I was just about ready to agree when a light suddenly turned into the tunnel ahead of us and started heading in our direction! Needless to say, we freaked. We all tore back up onto the platform and pressed ourselves into various corners of the station, only to realize that the train was turning onto a higher track to come into Upper Bay. Frankly, though, that was too little consolation to run the northern tracks without looking into their layout further, so Krall was disappointed once again as we executed a bathroomesque exit onto the upper platform and went on our merry way.
Suffice to say that the run from Museum to Lower Bay is a blast, and not as blatantly death-defying as some of the other things you could be doing in the tunnels (not that they don't have their respective charms). I'd recommend doing Lower Bay to anyone with an ounce of adventurousness -- it's a hell of an experience.
Woop!
Be sure not to miss the photo gallery, as it is highly nifty.

-Flame0ut