Strong winds and heavy showers are forecast to continue on Friday after Storm Ali kicked off the season with gusts up to 102mph that knocked out railways, roads and power lines.
Two people were killed, including a woman whose caravan was blown off a cliff in County Galway in Ireland.
A man, believed to be a contractor for Northern Ireland Water, died after a tree fell on him in County Armagh.
Substantial trees in full leaf were felled across southern and central Scotland, causing a nightmare for travellers.
A University of Dundee football team escaped serious injury when a tree crashed on to their coach at Kincaple, just north of St Andrews, where they were heading for a match.
One player is thought to have been slightly hurt.
A large golf marquee on the Old Course in the Fife town was lifted into the air and smashed by the winds.
A man was taken to hospital with a suspected fractured rib after becoming trapped beneath a digger in a river in strong winds at Rogart in the Highlands.
A “major incident” was declared in Dumfries and Galloway, where two schools were closed by falling masonry and flooding. More than 70,000 homes lost power and there were ten flood warnings in Perthshire, Ayrshire and Easter Ross.
Those travelling by air and sea were also hit, with more than 500 passengers aboard a cruise ship on the Clyde off Greenock rescued after it broke its moorings.
However, rail passengers were worst affected, with Scotland’s biggest stations at a standstill for a time and both lines to England also blocked.
Central and Queen Street in Glasgow, and Waverley in Edinburgh, were affected after felled trees and overhead line damage stopped trains on most routes across the Central Belt.
But there was also disruption in the Highlands after a freight train blocked the main line north when it hit a tree and derailed at Culloden.
ScotRail, which urged people not to travel, said because the trees had their leaves, they were more prone to blow over. Displaced commuters formed huge queues at bus stations in Edinburgh and Glasgow to get home.
Nathan Sheach, a designer for housing charity Shelter, tweeted: “Good luck to anyone trying to leave Glasgow for Edinburgh.
“I’ve attempted the [rail replacement] bus station twice and the queue goes round out of the building into the abyss, wind and rain.”
LNER managing director David Horne said trains were halted by two blockages between Edinburgh and York.
Virgin Trains services between Glasgow and London were stopped by problems between Motherwell and Carstairs, and north of Preston.
Airlines badly hit included Loganair, whose Edinburgh and Glasgow flights were suspended for a time.
The Tay Road Bridge was among those shut by the strong winds, where winds reached 102.2mph.
High-sided vehicles were barred from the year-old Queensferry Crossing for the first time amid gusts of 79mph.
The Forth Road Bridge, which now carries buses, taxis, cyclists and pedestrians, was also closed for a time.
There were also restrictions on the Kincardine Bridge in Fife, Friarton Bridge on the M90 near Perth and Erskine Bridge over the Clyde.
Vehicles blown over included a lorry on the M9 near Edinburgh. It rolled down an embankment and ended up on its side near the Newbridge roundabout.
Edinburgh City Council said more trees had blocked roads than in previous storms.
Princes Street Gardens was closed as a precaution, along with major routes in the city centre including Princes Street and South Bridge.
Police Scotland’s Edinburgh divisional commander Superintendent Richard Thomas tweeted: “Best to avoid Princes Street and areas around the Tron, High Street, where roads closures are in place due to loose masonry.”
In Dundee, one person was injured after being blown over outside the new V&A Museum on the city’s waterfront.
The museum stopped admitting more visitors because of the wind danger.
However, some workers carried on despite the conditions, including some leaf blowers outside flats in Glasgow.
New Gorbals Housing Association, which tweeted footage, observed: “Looks like these guys didn’t get the memo about #StormAli.”