Good point. Did any supplementary material ever detail Final Weapon, or was it just 'there' for the sake of the game's final levels?
In the regular eight levels, there was a train (which transported the building material), a jungle (to protect the weapon, possibly a decoy to throw off any enemy who dare to disrupt main construction), an arctic base (where the plans are stored), air force (to guard the core of the colony), cyberspace, laboratory (to possibly gather intellegence), volcaino (in pursuit of the traitor Magma Dragoon), and the marine base to quite possibly throw off X's trail/raid for supplies. Cyberspace was to test X as well as the first colonel fight in the memorial hall. The reploiforce began moving to space when the weapon was completed (thus the spaceport stage) and Colonel was sent to guard the station, being that stage's boss while the weapon was being launched into space (hence the weapon being shaped like a flower at a certain angle).