The Enterprise crew rediscovers the long-missing Bonaventure inside a space anomaly in the Delta Triangle in TAS: "The Time Trap". No date is mentioned as to when the ship was lost. Scotty's statement from the episode that the Bonaventure was "the first ship to have warp drive installed" is inconsistent with several accounts from live-action Star Trek, most notably "First Contact" where we actually saw the first (Earth) ship with warp drive, namely the Phoenix. In an attempt to reconcile the Bonaventure with modern Star Trek history and particularly with the already shaky development history of warp propulsion, his line may be re-interpreted in a way that she was more precisely the first starship with a modern warp drive like the Enterprise NCC-1701 has one. In any case Scotty's statement is unusually inaccurate, for he of all people should know exactly what warp drive actually means.
Pertaining to the Bonaventure's age, Spock adds to Scotty's discovery of the long-lost ship that "the crew's descendants may still be living", thereby implying that at least roughly a century has passed since her disappearance. Still, the re-interpretation in favor of a somewhat newer ship would work better in consideration of the Bonaventure's look which is not remotely like either the NX-01 or even the Phoenix but undeniably a disfigured version of the Constitution class. Even the markings on the vessel and the uniform patches are almost like in TOS. The Bonaventure has all the features of a Federation Starfleet ship, but how could the Federation be founded in the first place without warp drive? It is not the fault of the revisionist tendencies of modern Star Trek that the Bonaventure doesn't fit in, but it posed already a continuity problem at the time the episode was made. At that time the ship must have been intended to be more than 200 years old, so as to predate the unseen Valiant from TOS: "Where No Man Has Gone Before" which must have been a warp vessel.
To add to the confusion, Starfleet veteran Sarah April says she was "the first medical officer aboard a ship equipped with warp drive" in TAS: "The Counter-Clock Incident". While this is not exactly the same as "the medical officer on the first ship with warp drive", it still tells us that her service must have been soon after the launch of the Bonaventure, and possibly on the Bonaventure herself, luckily ending before the vessel's disappearance. It is just too obvious that a big ship like the Bonaventure would be in need of a medical officer just like any vessel of the NX-01 era too. So rather than being mistaken about the nature of warp drive like Scotty (which in her case would be rather forgivable), Sarah April may exaggerate a great deal. Or does she just mean she was the "first (=chief) medical officer" on no particularly important warp ship, which would pose no problem at all? This doesn't seem so, as she puts too much emphasis on "first", and Kirk agrees with her that she used to be a pioneer in space.
The matter is even more complicated because the first warp ship, as depicted in the first edition of the Star Trek Chronology, is shown in DS9 episodes on a wall display with the label "Bonaventure". The name is evidently a homage to the TAS vessel, yet along with a drastically different design. It is never readable on screen though.
The ship's length of ca. 212m results from a structural comparison with the Constitution class. At 212m the saucer rim (corresponding to two decks) is the same height on both vessels. The lower part of the saucer is the same size too, and it even has largely the same proportions which may be taken as further evidence that the Bonaventure can't be too old.
The Constitution class is the fastest and most powerful ship type of Starfleet.
Known ships
USS Enterprise NCC-1701
Annotations
The animated Constitution class must be essentially identical to its counterpart from the live-action series, the motion-controlled miniature, considering that the Enterprise is supposed to still be the very same ship. We should discount the slightly different proportions like the too long secondary hull, the deflector dish which looks like a cylinder rather than a bowl in the front view and the overall level of detail as shortcomings of the animated Constitution, notwithstanding that this vessel is still the most carefully drawn ship of the series.
Real differences to the TOS version can be found inside the ship. Most obviously the bridge has two turbolifts in TAS. While the single shaft was visible on the outside on the TOS Enterprise, there doesn't seem to be one on the animated version which, again, may be attributed to a lacking level of detail. Besides an engine room which is redressed once again since TOS, the animated Enterprise also has a impressively spacious room (TAS: "One of Our Planets is Missing") with tubes resembling the plasma conduits of later incarnations of Federation ships. Scotty is speaking of an "antimatter nacelle" though, which sounds like an awkward amalgamation of two components which should be distinct. If it is a part of engineering, we arguably haven't seen this part of engineering during TOS, although it certainly must have existed. Furthermore the Enterprise is equipped with what we could call a fully functional holodeck, here modestly designated as "Rec Room" (TAS: "The Practical Joker"). Aside from being inconsistent with statements about holotechnology being a very recent development in TNG, it is obvious that the Enterprise must have been refitted with such a rec room between TOS and TAS.
I assume that the arrowhead badges worn by the crew are still the same as in TOS, although they are not rounded in TAS and tilted to the left.
Cargo drones are automated vessels capable of warp speed.
Known ships
(Name unknown) NCC-G1465
Annotations
Two unmanned cargo drones were featured in TAS: "More Tribbles, More Troubles". They appeared to be a bit less than half as long as the Enterprise.
The design of the cargo drone, made into a CGI model and with a new crew module, was used for the USS Antares in TOS-R: "Charlie X". The same model, without the additional module and hence very close to the TAS ship again, appeared as the freighter Woden in TOS-R: "The Ultimate Computer".
The USS Huron belongs to a class of large Starfleet cargo ships. The vessels are weakly armed or unarmed.
Known ships
USS Huron NCC-F1913
Annotations
The Huron appeared in TAS: "The Pirates of Orion". A lower limit for the ship's length is 100m, as we can see it at some distance behind the Enterprise. Under the assumption that the nacelles are the same size as on the Constitution, the Huron is 260m long, and a lot more voluminous than the cruiser at this length. We obtain a more manageable size of 214m if we match the distances between the rows of (perhaps overly large) windows with those of the Enterprise.
Captain O'Shea identifies his ship as the "S.S. Huron" although we can read "USS Huron" on the hull.
The aquashuttle is a universal vehicle for space travel and maritime survey missions on the surface and under water. It is armed with two forward-mounted phaser cannons.
Known shuttles
(Name unknown) NCC-1701/5A
Annotations
An aquashuttle appears only in TAS: "The Ambergris Element" where it is destroyed by a sea monster. The fact that an obviously low-tech scouter gig (see below) is sent out to search for the missing aquashuttle indicates that there is only one aquashuttle aboard the Enterprise.
Most likely the aquashuttle hovers above the water surface similar to a present-day hovercraft.
The registry is barely visible. It could be NCC-1701/SA or NCC-1701/5A.
This shuttle is significantly larger than a standard shuttlecraft and probably designed for long-distance warp travel.
Known shuttles
Copernicus NCC-1701/12
Annotations
The Copernicus-type shuttle appears only in TAS: "The Slaver Weapon". It is possible that the screenplay which was penned by Larry Niven based on his novel The Soft Weapon called for a different, still larger type of shuttles than the ones already established in TAS.
The number NCC-1701/12 of the Copernicus is the same as of the heavy shuttle previously hijacked by Harry Mudd in TAS: "Mudd's Passion". It obviously replaces Mudd's shuttle which was eventually crushed by a rock monster. The presence of the Copernicus wouldn't leave much room for all the other small shuttles we saw in "Mudd's Passion" though.
Class specifications
Length: approx. 22m
Egg-shaped scout
General description
The scout is a small craft carried aboard Starfleet ships just like the shuttles too.
Known shuttles
No name given
Annotations
The scout is the vessel which is partially visible at the very right edge in TAS: "Mudd's Passion" and "Once Upon a Planet". According to Curt Danhauser's Guide to Animated Star Trek from where the sketches on the right are taken too, it was designed for TAS but never used in any episode.
Harry Fenton Mudd kidnaps Nurse Chapel and steals one of these shuttles (NCC-1701/12) in TAS: "Mudd's Passion". The shuttle type also appears in "Once Upon a Planet" in a brief shot. It appears to be somewhat longer than a TOS standard shuttle at about the same ceiling height. This shuttle is often referred to as "heavy shuttle" in fanon due to a lack of a more definite name.
There are two blunders in the episode involving the shuttle NCC-1701/12 that Mudd steals. At first this shuttle magically switches sides from the left to the right wall of the shuttlebay between two scenes. A few seconds later, when Spock looks at a display on which Harry Mudd, with Nurse Chapel, can be seen in the shuttle's doorway, the registry incorrectly begins with "N.C.C./" instead of "NCC-".
The scouter gig is a boat carried aboard Federation starships for missions on watery surfaces.
Known boats
(Name unknown) NCC-1701/R6
Annotations
The scouter gig can be seen only in TAS: "The Ambergris Element" where it is deployed to search for the missing aquashuttle which has been destroyed by a sea monster.
The hull of the scouter gig looks anything but hydrodynamically advantageous but may not have been built for high speeds anyway. It is does not become obvious how the scouter gig was transferred to the planet's surface. It was probably simply beamed down with a cargo transporter.
At least one of these shuttles with their characteristic flat tubular main body and top-mounted nacelles belongs to the inventory of the USS Enterprise.
Known shuttles
No name given
Annotations
The shuttle can be seen in TAS: "Mudd's Passion" and "Once Upon a Planet". It resembles the vessel owned by Carter Winston and could be of the same type. Only the nacelle arrangement may be somewhat different despite the inherent inaccuracies of the drawings. The shuttle appears to be somewhat longer than the standard TOS shuttle, but with a lower ceiling.
The registry on the drawing is conjecture; it was not recognizable on screen.
The scout craft is a small interstellar vessel for personal use.
Known shuttles
No name given
Annotations
Cyrano Jones was on such a "scout ship of common design", according to Spock, in TAS: "More Tribbles, More Troubles" when he came under attack by a Klingon battlecruiser. He was beamed out just before his vessel exploded.
Atmospheric vessels like this one were in use for planetary transport on Vulcan in the 2230s.
Known shuttles
No name given
Annotations
The desert flyer appeared in TAS: "Yesteryear". The vessel's size can be inferred from the seated figures inside.
Class specifications
Length: 7.6m
Vulcan ship
General description
This ship of Vulcan origin must have been in service during the 2240s.
Known ships
No name given
Annotations
We can glimpse the ship when the Guardian of Forever replays this era of Vulcan history in TAS: "Yesteryear".
Class specifications
None available
Vulcan shuttle
General description
The origin and exact purpose of this small vessel encountered on Vulcan in the 2230s is unknown.
Known shuttles
No name given
Annotations
We can spot the unknown shuttle on Vulcan in TAS: "Yesteryear".
Class specifications
None available
Unknown Class
USS Ariel, name of the missing starship in TAS: "The Eye of the Beholder"
We saw some crew members of the Ariel with exactly the same badge as that of the Enterprise (which doesn't make much sense because even the freighter Huron and the old Bonaventure have individual symbols). Anyway, the distinct badges of the Ariel depicted on some websites were made up under the wrong impression of looking different. But actually the Enterprise emblem is equally angular and tilted in TAS.