So, I don't have a full write up of this I'm happy about, but I figured I'd pitch it in general details for comments.
Long Island Rail Road and the Amtrak Long Island Mainline
Gauge: 4' 8.5''
Operational: 1834 - Present
Geographic/Pre-1900 Historical background:
The basic idea is that this is in a timeline where Long Island is an independent state of the United States, descending to the Revolutionary War era as a proprietary colony of Earl Stirling and his (ITTL surviving) descendants. It's established as an explicitly Scottish colony, favoring the Church of Scotland and later Scottish Presbyterianism, but because of the large number of Yankee settlers on the island already, there's a tradition of religious tolerance (indeed, looking at settlement, I'm questioning if the island is ever majority Scottish). The colonial capital of New Stirling is located at around the site of historical Port Jefferson and the (historical) colonial charter also grants all islands within five leagues (~28 km) of the island, so that would nominally include a bunch of islands in Long Island Sound like Block Island and Fishers Island, but also Staten Island and Manhattan. The latter is so core to New York that in the settlements of conflicting claims after New Amsterdam is absorbed in the 1660s that it's definitely staying with New York, but I'm amused by the thought of Staten Island ending up part of The Colony of Long Island and the New Hebrides and it's a bit of a secret tool that will helps us later.
IOTL, one of the later claimants to this title ended up settling in New Jersey, growing wine grapes, and fell in with agitators ending up a general in Washington's army. The idea of TTL is that an ATL equivalent of this guy is the brother of the current Earl at the time of the revolutionary war, and after some service in the French and Indian War or the like has settled at the family holdings out east of New Stirling, which IOTL is good wine country, and is up to much of the same stuff--revolutionary politics and wine. He ends up encouraging the colonial assembly into joining the Continental Congresses to seek redress of grievances, and when that fails, he ends up leading men from Long Island into Continental Service. During the war at some point, his brother and any nephews back in Scotland die in some late-18th century combination of sicknesses and accidents, and he inherits just in time to officially cede all the power to the colonial (turned state) government. All the titled holdings go to the state treasury, but a fair bit of the family holdings stay with the family leaving the Alexanders of Long Island very well off. This is also a secret tool that will help us...basically whenever the excuse of money is required.
The New Stirling and Brooklyn and the Origins of the Long Island Rail Road
The Long Island Railroad here is chartered originally as the "New Stirling and Brooklyn Railroad" around 1830ish - similar timing to the Long Island Railroad historically, but with an explicit goal to get service out to the capital. Construction proceeds faster than the OTL Long Island Railroad mainline, which historically was paused several times seeking investors and sufficient funding to complete the line, thanks to interest from the Last Earl's son, who had served in the army leading defensive forces on Long Island in the alt-War of 1812, and was frustrated continuously by the struggles of needing to bring logistics in by sea which the Royal Navy could occasionally threaten. A railroad offers an alternative which will build the industry of the state, and which is immune to naval blockade in the event of another war. The line is engineered to a high standard for the era, with smooth grades and large curves. It opens to New Stirling in like 1838 or 1839, and the line to Greenport with steamboat service to connect to railroads to Boston in 1840 or 1841. This grants a longer period of being the fastest NYC to Boston service, and to swing up to reach New Stirling, the line also serves more of the secondary communities of the North Shore. Later branches (or failed competitors absorbed over time as OTL) serve the south shore, but in addition to local freight and passenger service, the line wages a "time war" against the New Haven Railroad in Connecticut and the steamboats running directly from Boston to NYC for fastest and best passage from NYC to Boston.
The Long Island Railroad Reaches New York and the Mainland
Around the turn of the 1880s, the Brooklyn Bridge opens, connecting the city of Brooklyn, Long Island to its sister city of New York, New York. The Long Island Rail Road here senses an opportunity, and (with the aid of some of the Alexander money still floating around) construct a parallel span carrying four tracks for freight and commuter service into New York City, reaching a station around Canal Street with the bridge opening to traffic around 1895. Trains are hauled from Jamaica through Atlantic Terminal and into Canal Street Station by electric third rail power to meet Brooklyn against steam traction within city limits.
After the bridge, the next step for the railroad was a new route off the island, with the Narrows Tunnels constructed between ~1890 and ~1900, with two tubes carrying two tracks connection Brooklyn to Staten Island, and a link to the Baltimore and Ohio allowing for the first time for freight to leave Long Island by rail without trans-shipment. In exchange for allowing interchange services, the B&O also receive permission to bring trains up through Brooklyn to terminate in Manhattan, becoming the second mainland railroad to be able to do so after the New York Central/New Haven's Grand Central Station.
The New York Union Railroad
In the 1890s, with the PRR planning a line connecting directly into New York, negotiating with the LIRR and the New Haven for the creationg of a New York Connecting Railroad linking the PRR tunnels, a new Hells Gate Bridge, and the existing LIRR Narrows Tunnels, and with the Central outgrowing their terminal at 42nd Street and planning a major and disruptive rebuild, New York Government makes everyone wear their "get-along" shirt together and creates the New York Union Railroad. This consists of a two-level station at Union Square, with the lower level being for the PRR's east-west tracks (crossing here at 14th street, not 33rd street) while the upper level is for a new extention linking fro m14th Street north along Park Avenue to the Central's existing station and south to Canal Street and the LIRR's terminal (shared with the B&O). This Union Station will allow passengers maximum ability to transfer trains, and is forced upon the railroads with the promise of better connections for passengers into the city, both for commuter and logn distance services. This replaces Penn Station and the 1910-era (still standing IOTL) rebuild of Grand Central Station, which here is much more modest as most trains through-run down the new tunnels on to terminate at Union Station or even run through to Atlantic Terminal and the LIRR yards there (by contrast, many LIRR and B&O trains run through Canal Street, Union Station, and up to Grand Central to terminate in the Central's Yards there - effectively, swapping yards). Getting the tracks built is obviously a giant nightmare, and the exact number of platforms and tracks is TBD, but it's a magnificent station with separate headhouses for the PRR, Central, and LIRR, with a large glass roof over a "hanging garden" providing light down to the upper platform level in the middle of Union Square, the clean glass an implicit brag about the electric traction with which all trains serve the station.
The "Stirling Folly"
A new generation of Alexanders had led the LIRR's board through the construction of the Manhattan Bridge, the Narrows Tunnels, participating in the New York Connecting Railroad and the New York Union Railroad, opening Union Square Station, electrification and speed improvements to 100 mph running along effectively all of the LIRR's mainline on Long Island, acquisitions of small shortlines off the island enabling connections as far away as Buffalo, and had developed a fair sense of empowerment and technical skill that led to a desire to challenge mainline and mainland railroads like the Central, the New Haven System, and the PRR. Running high on money and technical skill, he sets out for the Long Island equivalent of Flagler's "Overseas Railroad" - the Race Tunnel. It would run on new alignment from Greenport, LI to Orient Point, then on viaduct over water to Plum Island where it would descend into a tunnel (ventilation duct and construction access at Great Gull Island to descend under the Race at the east end of Long Island Sound before rising to the surface again at Fishers Island, Long Island (one of the New Hebrides) and cross to the mainland at New London. The main tunnels would be almost 8 miles long, but provide a link to turn the LIRR (along with some railroads acquired in Rhode Island and Massachusetts) into a high-speed mainline alternative for NYC to Boston passenger and freight traffic, challenging and indeed usurping the railroad's longtime rival of the Ne Haven System. Construction was begun after much engineering evaluation in 1912, with a pilot shaft dug first followed by the two main track tunnels through. It takes...years and years, and the project becomes knows as "the Stirling Folly," with one cartoon depicting the instigator as King Canute ordering around the tides, or Caligula ordering the sea whipped and declaring war on Neptune himself. The tunnel is delayed by manpower and equipment during WWI and the immediate post-war economic instabilities including the Flu, but finally around the mid-20s the tunnel is finished, track is laid, electrification and substations are in place, and for the first time high speed trains can run from NYC to Boston in speed and comfort at average speeds exceeding 70 mph, and rising over the 30s to 80 mph, dropping the running time of the "Meitowach Express" service from three and a half hours to under three - a running time which in the railroad's earliest years would not have sufficed to even reach New Stirling from Brooklyn.
Cashflows and the 1960s
The peak of the LIRR like other railroads comes with the 30s and 40s. After WWII, the automobile and the truck increasingly take over, and like other Northeastern railroads the LIRR suffers. In the 1960s High Speed Ground Transportation investments, the LIRR's mainline gets a lot of attention alongside the PRR line NYC to Washington and the New Haven's line from New York to Boston. I'm imagining that like the New Haven had their association with the UAC Turbo and PRR had the Budd Metroliner, the LIRR have their own funded HSR proposal--maybe they get an electric version of the Turbotrain, or maybe it's their own design. I'm ignoring a lot of butterflies to get here, but the alignment in my head is capable of 150+ mph on land and 80-90 mph in the Race tunnel, and thus average speeds from NYC to Boston on the LIRR northern mainline is maybe 125 mph or so? A target time of 2 hours from NYC to Boston could be feasible. However, with how hollowed out all the lines were, I'm assuming some kind of collapse eventually comes, even if the LIRR avoid being sucked into the Penn Central and ensuing explosions. Something like Amtrak is formed, and the LIRR turns over their money-losing long distance express trains to Amtrak and the money-losing commuter trains to the Long Island State Transit Authority. This is the corporate parent of the LISTA Rail commuter trains and Brooklyn Rapid Transit subway services, though both are technically interstate with service into Manhattan as well as serving Brooklyn and its boroughs of Queens and Staten Island. Brooklyn is the largest city in the US by population, but a fairly significant fraction of that population commutes into the sister city of New York City for work.
1970s to Present
In the present, the original LIRR northern route is the Amtrak "Long Island Main Line" serving fast express trains from NYC, Brooklyn, New Stirling, New London, Providence, and Boston, which make the run with modernized equipment running up to 180+ mph on portions of the alignment to make the trip overall in well under 2 hours, while something more like the Northeast Regional plies the legacy New Haven Connecticut lines, topping out at about 125 mph. Local island needs and commuter service is provided by LISTA Rail, with service into New York Union Square Station and stations at Atlantic in Brooklyn, Canal Street in NYC, and all the way up to Grand Central Station at 42nd. Maybe at some point a loop line connection through an alt-63rd Street Tunnel allows the Grand Central trains to keep running and loop around through Long Island City and Sunnyside to avoid needing to turn around trains in NYC at all? The upcoming need to overhaul or replace the Narrows and Race Tunnels is a major discussion topic in the State House and Long Island's congressional delegation.