It's the afternoon, there is a breeze in the air, clouds are all over the sky, dark clouds that announce a storm is coming. This is how the story of The Dig begins. Which was quite different as how, the history of The Dig really happened…

It all begun in 1989 when Steven Spielberg started to show interest in computer games. He was (and still is) a friend of George Lucas and he was very happy with Indiana Jones and the Last Crusade (made by LucasFilm Games).
Around that time he brought to LucasFilm his idea for The Dig, which was based on two main concepts. The first was originated by an idea he had for an episode of his Amazing Stories TV series (that due to budget and technology reasons was never filmed). The second concept was a merge of ideas coming from two films: Forbidden Planet and Treasure of the Sierra Madre. These two concepts were the base for the beginning of The Dig.

The first project leader was Noah Falstein (read his interview here). Part of the team for this first version was: Dave Grossman, Ken Macklin, Anson Jew, Terry Whitlach and Iain McCaig among others.
The game was described as a "Science Fiction Role-playing Adventure". The main characters (from which you could choose) were a man called Terasov (an engineer) and a woman called Fox (a biologist). The story took place in the future; the characters were part of the crew in a spaceship assigned to explore an unknown planet which was apparently desolated. Eventually you find out that aliens who lived in this planet haven't died…

You can read the original game script/description in the downloads section.

Noah Falstein worked on The Dig for about 18 months and after a series of events he eventually was laid off. Before this, Brian Moriarty had been already assigned to The Dig project and he decided to start from scratch.

In 1993 the second project leader, Brian Moriarty (Creator of Loom and the Infocom text adventures Wishbringer and Trinity), again took some of the Spielberg's original concepts and created a new story. This story is at least 80% of the one you have played in the released version. It occurred in the present (or near future) and this time it was an Adventure game. This was a much deep and serious version than the one it was released; it was also more bloody and violent.
Bill Eaken developed the artistic style of the game and did most of the backgrounds. He was the one who came up with the idea of the spires. He sketched them up in a rough concept and Brain saw those and thought they were interesting and that the whole game should take place just on these spires. Moriarty wanted no plants or structures on the islands, just rocks. Bill was worried it would be boring so he came up with two elements that would help make the rocks less boring: bright color, and the alien rock carvings. Bill Tiller (lead artist on the released version of The Dig) took these themes and pushed them even further, adding even more cravings, even some plants, and lots more water and water falls. The color, the water effects, the vistas, and the alien rock carvings al gave this new Dig a unique and appealing style, despite the stark landscape.

In this version there were four main characters: Boston Low, Dr. Ludger Brink, Judith Robbins, and Toshi Olema, a Japanese businessman who provided much of the funding and technology for the shuttle mission, since NASA was at an all-time budgetary low.
Because there was an extra astronaut, the box art showed four characters instead of three, as seen on the cover of Adventurer #6 and on the audio-book of the novel. This fourth spacemen was later photoshoped out, by the time the package was being designed (read the interview with Blind Mice Studio here)
(Interestingly, Olema is not an actual Japanese last name. Brian Moriarty remarked to other team members that he had a funny background story for it, but it's never been revealed. Also, the idea of an executive from Japan funding an entire shuttle mission is based on the early 1990's fear in America of the rise of Japanese industry. One of the influences driving Moriarty to use the concept was Michael Crichton's novel Rising Sun)
The aliens saw the multi-dimensional reality to which they had ascended as a paradise, since it allowed them to live forever (they weren't trapped in it, as in the final Dig). They wanted to share it with others, but only those who proved their worth. So when other races began to explore space, these aliens would send an asteroid to their planet, as the first step on the journey into this higher plane. But in order to enter the aliens' reality, beings had to have their subatomic particles flipped.
Such flipping was accomplished by passing through a four-dimensional tubular shape, known as a "Klein bottle," which was apparently contained somewhere in the asteroid. The Klein bottle would cause all four crewmembers to become left-handed before they arrived on the alien planet, and the game's artists had to animate them in that manner.
The alien world had been intentionally designed to be dangerous; the whole place served as a test to find out whether new arrivals were clever enough to survive and find their way into the aliens' higher plane. Like in the final game, the aliens would occasionally show up in the form of "ghosts" to guide the crew. In Moriarty's The Dig they were orange in color, but in the actual release they're blue.
Some of the puzzles and plot ideas were much more violent than anything in Sean Clark's version. For example, Toshi Olema was killed after walking through a cave filled with falling acid drops, leaving behind a bloody, mutilated corpse. Also, Judith Robbins was attacked by a swarm of fierce bats.
One puzzle required Low to get rid of some bats who were blocking the entrance to a cave (perhaps so he could rescue Judith). An eel caught bats to eat by emitting a beam of green light from its eyes which stunned them, so they would fall to the water below. Low had to electrocute the eel, cut out the lens of its eye, put the lens on his flashlight, and shine the light at the bats; then the creatures would drop to the cave floor.
Life crystals apparently existed in Brian Moriarty's design for The Dig, and drove Brink insane, as in the final game. It was in this version that cutting off Brink's hand was first thought up; in the original idea, the tide was rising in the cave where he was stuck, and he had to be freed quickly to save him from drowning. While the basic puzzle remains in the released Dig, there's no water involved.
Spielberg himself asked for these violent and gross scenes, since he had done similar scenes in movies such as Jaws, Indiana Jones and Jurassic Park, but after Jurassic Park came out, Spielberg was heavily criticized for the violence in the movie, due to that fact many parents ignored the PG rating and inappropriately took very young children to see it because it had dinosaurs in it. Spielberg was concerned that the same would happen to The Dig that parents would buy it for young children. So he called LucasArts up and asked them to tone it down.
Moriarty's game was controlled by a 4-icon GUI which resembles the one in Sam and Max Hit the Road, with icons representing the actions Examine, Pick up, Use, and Move. The game wasn't being made with the usual SCUMM system, but was going to use a new engine that was being developed called StoryDroid.

The heavy emphasis on scientific details in The Dig's story worried LucasArts marketing, and the game was unpopular inside the company due to it unusual development length and due to the unusual amount of publicity it was getting. Many felt better games were in development at LucasArts but weren't getting near as much press or interest. Eventually, when Brian Moriarty became very unhappy with the development of the game for many reasons, he left the company to go work at Rocket Science (in fact he left LucasArts the same day that the Pizza Orgy for The Dig was being held). Rumors went around about why Brian quit, but most agree it was an incredibly stressful Project, due to Spielberg's name being attached and due to amount of art that need to be generated for it. Brian's past experience in text based game making had not prepared him for developing such an animation and art heavy project and with such a large staff. The added stress of developing a replacement for the SCUMM engine didn't help either.

The third project leader was Dave Grossman, who picked up where Moriarty had left. He made some fixings to the game while trying to retain as much as possible of the Moriarty version. The company was not going to allow him to start a completely new version. Dave worked on The Dig for a few months, until Sean Clark came in fresh from his succesful project Sam and Max hit the Road.

Clark was the person who finally managed to finish the game, in 1995. He made some major changes, including removing Toshi Olema entirely and changing Judith's name to Maggie (as a reference to a character on the TV series Northern Exposure).
The game engine was switched from StoryDroid back to SCUMM, LucasArts' standard, because that was the engine Sean knew best and felt at this point The Dig needed to mitigate as many risk as possible. The character designs also were redone (by Geri Bertolo). And the aliens' backstory was greatly simplified (to management's relief).
Although early beta versions of Clark's The Dig included a 5-icon GUI much like the one in Brian Moriarty's version (but with an extra Talk to icon added), it was later simplified to the final "one-click-does-it-all" interface, after the former was deemed too cumbersome by testers.
(Some team members experimented with a Full Throttle- and Curse of Monkey Island-style "verb coin" control method, using a sheer glass pentagon with the five icons arrayed around it. But Sean rejected the idea, because he didn't want to copy another game.)
During testing, the original space puzzle was simplified considerably. The player originally had to take the Pig to the asteroid surface; return to the shuttle and carry the explosives back to Attila; and then radio to the shuttle to have Ken and Cora scan the asteroid for the devices' proper positions.
The voices in The Dig's demo, quite different from those in the actual release, were once intended to be used in the final game. However, during production on Sean Clark's design, almost all of the dialogue was rewritten after being recorded. During the re-recording process, LucasArts decided to hire new, more professional voice actors.
The original lines were recorded at a time when the 5-icon interface was still being used. If you explore the demo's audio files, you can find references to the various commands (such as Low saying "I wouldn't want to be pushy" in response to the command Move Brink or Move Maggie).
Also, during the rewriting, some of the scientific details in dialogue were simplified. For example, in the demo, Low notes that a plant is respirating if you click on it. In the final game he worries that the plant might be something like poison ivy.