Indiana Jones and the Iron Phoenix
One of two failed planned sequels to Fate of Atlantis, Iron Phoenix got furthest before the plug was pulled. The story involved Russians, post-war Nazis hiding in Bolivia trying to resurrect Adolf Hitler with the power of the Philosopher's Stone, a mysterious Tibetan monastery and otherworthly guardians watching over parts of the Stone. There are clearly several plot-points here that were carried over to the true Fate of Atlantis sequel, Infernal Machine.
The game was being developed between 1993-1995 before it was cancelled due to various reasons. There were many clashes in art style between developers for a start, such as Anson Jew wanting the design to be stylised Art Deco style but background artist Bill Stoneham wanted a more realistic approach. FMV for cutscenes was also considered, which was clearly a very bad idea as Harrison Ford was never going to do it.
LucasArts were also supposed to make the game with a Canadian developer, but this company wasn't very skilled at programming or creating art so that didn't help. But the death-knell for Iron Phoenix came after European trade show ECTS, where LucasArts showed the game and learned that Germany (the biggest market for adventure games) would never allow a game that explicitly showed Nazis. Other Indy games got away with this by covering up the references, but Nazis and Hitler were a main part of Iron Phoenix's plot. So sadly the game was cancelled outright.
The story was adapted into a four-part Dark Horse comic series, which will shortly be available again as part of the Second Indiana Jones comics Omnibus, available June 25th 2008.
After Iron Phoenix's sad cancellation, LucasArts looked into another potential storyline. Apparently lead by Aric Wilmunder (who was one of the project leaders on Iron Phoenix before he dropped out), the story involved Indy versus Nazis again, this time in a hunt for the Spear of Longinus, the artifact that pierced Christ's side during his crucifixion (then his blood was caught by the Holy Grail). However, LucasArts once again tried to farm a lot of the development out to the same Canadian company that failed Iron Phoenix, so the project was doomed almost immediately.
Indiana Jones book author Max McCoy once revealed in an interview that he wanted to write a Spear of Destiny story for Indy, but wasn't allowed to because LucasArts had a game in progress using the Spear. This is how we found out about the game's existence. (McCoy would go on to use a Crystal Skull instead!)
Like Iron Phoenix, this game's story also produced a Dark Horse comic series, which also featured the welcome reappearance of Sean Connery's Henry Jones Snr. Whether the comic's story bears any relation at all to the one by LucasArts is anyone's guess. It will soon be available in the same Omnibus book as Iron Phoenix, linked above.
What is most interesting about Spear of Destiny is that this artifact has actually supposed to have been found, and more than that, was found by the Nazis! Indeed, this was probably the basis for the whole "Hitler hunting for religious artifacts" idea that spawned Raiders of the Lost Ark. The Spear of Destiny (or 'Holy Lance') can nowadays be seen in the Schatzkammer museum in Vienna.
Indiana Jones and the Garden of Life
Now this one got even less far than Spear of Destiny, and for good reason. However, this one was meant to be the follow-up to Last Crusade rather than Fate of Atlantis. After the success of Last Crusade, LucasArts wanted to make another Indy adventure.
The best idea available to them unfortunately was a rejected script for the third Indy film, by Chris "Harry Potter 1 & 2 and not the guy who discovered America" Columbus. This was titled either Garden of Life or (gulp) Indiana Jones & The Monkey King. Based on the legend of the Chinese Monkey King who had a garden of immortality peaches (yes, really), Columbus's script has tons of action, and all of it ludicrous. A rhino chase and a 100-foot tank battle are just two examples.
It was clearly an awful script that never would have worked as a film, let alone a game. Thankfully, Hal Barwood and Noah Falstein realised this early on, gave up on the script and came up with Fate of Atlantis instead. And the world is still grateful.
Indiana Jones 2007
Just kidding. UPDATE: Maybe I shouldn't have posted this here, I might have jinxed things.
There are many rumours as to why "Indiana Jones 2007" (which LucasArts does not officially admit is the 360/PS3 version of Staff of Kings) was cancelled, but the only thing official is that LucasArts management wanted it 2009 and there was no way it was going to make that. So it was cancelled and Staff of Kings, which LucasArts always intended would lead on the Wii because it's such a perfect fit with all the whipping and everything, appeared magically out of thin air. As games do.
Read about the Iron Phoenix comic here!
Read about the Spear of Destiny comic here!
See the real Spear of Destiny here!
Read the supposed Garden of Life script here!
Or read about it and other failed Indy IV ideas here!