The main rail routes in Scotland connect the seven cities together. There are many services between Edinburgh and Glasgow, and from those cities trains run to Stirling, Perth, Dundee, Aberdeen and Inverness. All of these cities have direct services to England - Edinburgh and Glasgow have many to the rest of the UK.
There are also train services to large towns such as Dumfries, Lanark, Galashiels, Livingston, Coatbridge, Cumbernauld, Falkirk, Alloa, Dunfermline, Kirkcaldy, Arbroath and Fort William. The Caledonian Sleeper provides an easy, overnight route from London to both the Highlands and Lowlands.
Trains meet the ferries at Ardrossan, Largs, Wemyss Bay, Gourock, Oban, Arisaig and Mallaig, and the station at Thurso is a short taxi trip away from Scrabster ferry terminal.
There are plenty of scenic rail routes, including:
-the Borders Railway from Edinburgh to Tweedbank
-Glasgow to Oban past Loch Lomond
-Glasgow to Mallaig, over the Glenfinnan Viaduct
-the main route to Inverness through the Cairngorms
-Inverness to Kyle of Lochalsh via Plockton
-Inverness to Thurso and Wick - 'The Far North Line'
There are also sometimes steam trains on the spectacular line over the Glenfinnan Viaduct between Fort William and Mallaig on The Jacobite.Bus:
If you're travelling by bus, then the main operators are Lothian Buses, Stagecoach, First, and Scottish Citylink. Lothian Buses operate the flat-fare Edinburgh network. Stagecoach and First provide many of the main regional routes in Scotland, while Citylink provide longer-distance coach services. These connect together the main cities, and the company also provide the main routes to Skye, Fort William, Loch Ness, Lochgilphead, Campbeltown, Cairnryan (for the Stena Line ferry to Belfast), and Ullapool (for the CalMac ferry to Stornoway) among other locations.
There are also many other bus operators in Scotland that run local services. I've listed some of these below; these are the ones that you may find the most helpful to you.
Caledonian MacBrayne is the main ferry company to all islands except Orkney and Shetland. NorthLink Ferries run the services from these two archipelagos to the mainland. Orkney is additionally connected to the North Highlands by Pentland Ferries (this route provides the fastest car transfer) and, in summer, by passenger-only services run by John O' Groats Ferries (this crossing is the shortest overall, but rather leaves you on the edge when it arrives in Orkney, so is generally used only by those on Orkney Day Tours).
Scotrail (for all services in Scotland): https://www.scotrail.co.uk/
Caledonian Sleeper: https://www.sleeper.scot/
Virgin Trains East Coast (for services to Newcastle, York and London): https://www.virgintrainseastcoast.com/
Virgin Trains (for services to the Lake District, Lancashire, Birmingham and London): https://www.virgintrains.co.uk/
TransPennine Express (for services to the Lake District, Lancashire, Manchester and Manchester Airport): https://www.tpexpress.co.uk/
CrossCountry (for services to Newcastle, York, Yorkshire, the Midlands and the South West): https://www.crosscountrytrains.co.uk/
The Jacobite Steam Train: http://www.westcoastrailways.co.uk/jacobite/jacobite-steam-train-details.cfmBus companies:
Lothian Buses (buses around Edinburgh, and to Penicuik and North Queensferry): https://lothianbuses.co.uk/
Scottish Citylink: http://www.citylink.co.uk/
East Coast Buses (Edinburgh to Musselburgh, Gullane, North Berwick, Tranent, Pencaitland, Haddington, Easy Linton and Dunbar, and Musselburgh to Penicuik): https://eastcoastbuses.co.uk/
Border Buses (operate the main routes from Edinburgh to Peebles, Galashiels, Selkirk, Hawick, Melrose, Kelso and Jedburgh): https://www.bordersbuses.co.uk/
West Coast Motors (for services to Campbeltown, Tarbert (Loch Fyne), Lochgilphead, Oban, Inveraray, Rothesay, Dunoon & the Isle of Mull): http://www.westcoastmotors.co.uk/
McGill's (for Inverclyde, Renfrewshire and Monklands - operates a through route from Glasgow to Dunoon): http://www.mcgillsbuses.co.uk/
Xplore Dundee (for buses in Dundee city): http://nxbus.co.uk/dundee
Buses on Skye and in Orkney are run by Stagecoach.
Buses in Shetland: http://www.zettrans.org.uk/bus/BusTimetables.asp
Buses on Islay: https://www.argyll-bute.gov.uk/isle-islay-portnahavenport-askaig-bowmore-port-ellen-ardbeg
Buses on Jura (route 456): http://www.garelochheadcoaches.co.uk/timetables/
Buses in the Outer Hebrides (including the Overland Route): https://www.cne-siar.gov.uk/roads-travel-and-parking/public-transport/bus-services/
Long-distance coach companies:
These largely connect the major Scottish cities to England, although it is possible to use these services to travel between Scottish cities.
National Express: https://www.nationalexpress.com/en
These connect Edinburgh city centre with Haymarket, BT Murrayfield Stadium and Edinburgh Airport. https://edinburghtrams.com/
Caledonian MacBrayne: https://www.calmac.co.uk/
Western Ferries (McInroy's Point to Hunter's Quay, the car ferry route to Dunoon): http://www.western-ferries.co.uk/
Argyll Ferries (the direct route from the centre of Gourock to the centre of Dunoon, but passenger-only):
NorthLink Ferries: http://www.northlinkferries.co.uk/
Pentland Ferries: http://www.pentlandferries.co.uk/
John O' Groats Ferries (summer only): http://www.jogferry.co.uk/Home.aspx
Orkney Day Tours (summer only): http://www.jogferry.co.uk/Tours.aspx
Arisaig Marine (Arisaig to Rùm, Muck and Eigg, summer only): http://www.arisaig.co.uk/
Corran Ferry (Corran to Ardgour): https://www.highland.gov.uk/info/1526/public_and_community_transport/776/corran_ferry
Cromarty Ferry (Cromarty to Nigg, summer only): https://www.highland.gov.uk/info/1526/public_and_community_transport/777/cromarty_ferry
Kilcreggan Ferry (Gourock to Kilcreggan): http://www.spt.co.uk/kilcreggan-ferry/
Knoydart Ferry (Mallaig to Inverie, summer only): https://westernislescruises.co.uk/knoydart-ferry-timetable/
Jura Ferry (Feolin, Jura to Port Askaig, Islay): https://www.calmac.co.uk/article/3131/Port-Askaig---Feolin
Jura Passenger Ferry (Craighouse, Jura to Tayvallich, Argyll, summer only): http://www.jurapassengerferry.com/
Other ferries go from the mainland to the Isle of May, the Summer Isles, Bass Rock and Handa among other places. These are all summer-only I think. I've only included the main ferry services above - Scotland has many boat services that will take you to our little islands and on wildlife-spotting trips, where you can look out for dolphins, seals and seabirds.