Eggman's Space Armada is a fleet of space ships built by Dr. Eggman, presumably so the Eggman Empire could cause terror from the skies of Mobius. They met their demise at the hands of Super Sonic, who made "mincemeat" of the armada and confronted Eggman himself on what appeared to be the last remaining space ship. Eggman then "surrendered" to Sonic who turned to leave, but Eggman activated a machine on board the ship that drained the power out of Sonic and the Chaos Emeralds, and used said power to fuel a weapon to shatter the world and unleash "it". This also caused Sonic to transform into a creature dubbed the "Werehog", which terrified Eggman and caused him to toss Sonic out into space with the drained Chaos Emeralds. (StH: #193)
Although never seen, it is made obvious by the fact that the story the Space Armada appeared in was an adaption of the following game, and that these ships are the same ones that appeared in the opening scene of Sonic Unleashed.
In Sonic X, Dr. Eggman has released the Death Egg and now Sonic and Tails must stop him. However, their new airship only supports 1 passenger, and to defeat Eggman they need the 7 Chaos Emeralds. Misty said that the Space Armada is protecting the Death Egg.