The game's narrative framing device is that it is a comic book being read to the player. The story opens in a steampunk fantasy version of London on the opening day of the Steamgate Bridge.[8] Henry Fleming (based on the protagonist of the same name from the novel The Red Badge of Courage and voiced by Adam Baldwin) is going over security detail at the American Embassy, when suddenly the city is attacked by an unknown enemy force. He manages to escape and meet up with his old friend John Henry (voiced by Michael Dorn). The two are then rescued by an airship called the Lady Liberty, captained by the once-presumed-dead President Abraham Lincoln (voiced by Wil Wheaton).[13] He explains that the city is under attack by aliens and conscripts the two into the strike force S.T.E.A.M. (short for Strike Team Eliminating the Alien Menace).[8][14]
After rescuing Queen Victoria with the help of Lion (voiced by Fred Tatasciore) from The Wonderful Wizard of Oz, Tiger Lily from Peter Pan (voiced by Kari Wahlgren), and Tom Sawyer (voiced by Jeremy Shada), the soldiers are eventually forced to leave England to its fate and retreat to America. They are delayed by a giant monster that is defeated by Lincoln himself in his giant mech, the A.B.E. (Anthropomorphized Battle Engine). They swing by Boston in order to help the forces there and meet up with Queequeg (voiced by TJ Storm). They then receive a distress call from Professor Randolph Carter (voiced by James Urbaniak) of Miskatonic University, S.T.E.A.M.'s expert on the occult. They meet Lion's friend Scarecrow (voiced by Paul Eiding) on the way there and manage to evacuate the university with Carter in tow. However, before they can get on the Lady Liberty, Carter's notes are taken by a mysterious creature called a Starface who then flees the scene.
Carter says to Lincoln that the aliens were not just after his research, but also the Necronomicon which has led to numerous discoveries that have improved technology manifold. It was kept at Miskatonic until recently and the team sets forth for its current location: 1600 Pennsylvania Avenue, directly under the White House. They manage to get to the White House, meeting with dashing thief the Fox (voiced by Grey DeLisle) and warrior queen Califia (voiced by Kimberly Brooks). While they do keep the Necronomicon from the hands of the enemy, they unfortunately have to abandon the capital.
With the Necronomicon, Carter concludes that the source of the threat is the Great Shugguth, a creature that can perpetually create soldiers, left behind by the aliens 200 million years ago for reasons unknown. The Shugguth is buried underneath the South Pole so the team stops by Monument Valley to repair and refuel. However, their base comes under attack and they barely manage to escape with the help of the cyborg Tin Man (voiced by Andrew Kishino) and Lincoln critically injured.
When all hope seems lost, a strange light appears in the Lady Liberty, revealing none other than Dorothy Gale (voiced by Amber Hood) who takes the team to Oz which is also under attack. They save Queen Ozma whose engineers at Oz manage to upgrade A.B.E. so it is capable of drilling through the ice in the South Pole as well as giving them emerald keys so they can teleport instantly between two points in space. Returning to Earth, they hear from General Ulysses S. Grant that half the planet has been frozen over and that they are running out of time.
Fighting through the aliens' lair, they manage to confront the Starface and defeat it, though the Shugguth turns mad and goes on a rampage. Lincoln faces off against the great beast, but in its death throes it intends to take out the entire planet. Lincoln then self-destructs A.B.E., destroying the Shugguth but at the cost of his own life. With the planet saved, S.T.E.A.M. pays their final farewells to Lincoln, throwing a bouquet into the great chasm where he made his last stand and are joined by other airships doing the same. A post-credits sequence reveals Lincoln's stovepipe hat, but an emerald key is nearby, hinting that he may have survived. The comic is then turned over to its final pages, revealing a new story arc is coming.