Those of you who are fans of Star Trek: The Next Generation may recall an episode called "Yesterday's Enterprise." This scenario follows a similar plot line. The adventure calls for role-playing more than action, though there is plenty of that as well. The party should be experienced, having logged a lot of time in space. It would also be good to have someone on the ship with a strong knowledge of history, like a sage or a bard.
The adventure begins with the PC's ship approaching a major world like Toril, Krynn, Oerth, or some other world that plays a prominent role in your campaign. All appears to be well, until a huge multi-colored field appears above the southern hemisphere of the planet, and the great Spelljammer itself appears out of nowhere! This will certainly catch the PC's attention, if not because of the jammer, then the field from which it came.
The Spelljammer will come to a slow stop, about 1000 miles from the PC's ship, and just hang there, motionless. Point out that the PC's have a golden opportunity to study the ship from a distance. If one of the PC's (or NPC'c) on board has seen the Spelljammer before, tell them that it doesn't look "right" somehow. The colors are wrong, the citadel doesn't look exactly the same, whatever.
The PC's could fly right up to the Spelljammer if they want; it will make no attempts to capture them. In truth, it isn't interested. It's too busy healing itself from a recent ordeal. After a while, the PC's lookout will raise a very frantic alarm: a fleet of Neogi ships is coming from the planet below and is closing on the Spelljammer, and the PC's! The fleet is HUGE: about 24 Deathspiders and twice that many Mindspiders, all swarming up from the planet. Apparently the Neogi rule the planet below.
"Hey, wait a minute! That planet is inhabited by friendly races, not Neogi!" exclaims one of the characters.
As the Neogi close with the Spelljammer, the great ship will seize the PC's ship with the magical equivalent of a tractor beam, and secure it near the stinger. It will then head for the flow as fast as it can. The neogi will give up the chace after about an hour.
The PC's and their crew will be taken aboard the Spelljammer and tended to. Note that they will not be captured by the ships aura: the captain of the Spelljammer is deliberately preventing that from happening.
As the Spelljammer assumes a leisurely course to the flow, the PC's will certainly be curious about the Neogi fleet. They will learn the following (role play this if possible):
The PC's now have to convince the captain, and the great ship, to go back in time and engage the Neogi, as they should have done. Obviously the idea won't be very popular, but the alternative is too horrible to ignore, even for something like the Spelljammer.
In the end the Spelljammer will create another time rift and go back in time - taking the PC's with it! (This is purely to make them nervous, for the GM's benefit) The ship will return to the planet, just in time to see itself vanish into the future...
The neogi are now off guard, since their prey had escaped. Surprise! The Spelljammer will move right into the pack of ships and nail them with everything it has. After a few minutes, the PC's will be teleported back to their ship and told to leave, NOW! ("Where we are going, you can not follow" sort of thing). If for some reason their ship has been destroyed, a Smalljammer will be provided. In the confusion, the PC's will be able to slip away and enter the time rift.
For dramatic effect, have them look back through the rift just before it closes, to see the Spelljammer explode in an inferno of fire and debris, taking most of the neogi fleet with it. The rift will close, leaving the PC's in the original timeline, with everything back to normal: the past has been restored.
The Neogi have not attempted to conquer an entire planet since. This defeat, at the hands of the Spelljammer, is a loss from which the Neogi have never truly recovered.
As for the PCs, their ship will go back through the rift and they will emerge at approximately the same time the left (give or take a few minutes). The rift will remain open long enough for the PCs to escape, but only that long.
Of course, things need not turn out this nice. If the GM wants to turn the entire campaign upside down for some reason, this scenario could be used to throw the characters into an alternate time line. This may be difficult to set up, but it will certainly keep the players awake.
One could also work things such that the Spelljammer keeps running after emerging from the rift, so it may take a while for the PCs to figure out what has happened. This could lead to a multi-adventure chase of the great ship, with an ultimately tragic ending.
Finally, this could be a way to introduce time travel into a campaign. An entire sub-campaign can be developed while the PC's try to figure out how the Spelljammer created the time rift, and perhaps try it themselves one day. Only a very experienced GM should attempt this, but an entire new dimension (pardon the pun) could be added to a campaign this way.
GURPS Time-Travel, by Steve Jackson Games, gives a lot of useful advice for running a time travel campaign. If a GM really wants to try this, that work is strongly recommended. Time travel in a fantasy universe can be trickey, since there is no "real" frame of reference, like there is in the time travel stories of our own Earth. However, the timeline that appears later in this work could serve as a good springboard for this type of campaign.