Enterprise's Cargo Bay Two became affected, in 2153, by spatial anomalies that were a characteristic of the Delphic Expanse, causing cargo to fly from one wall to another and cling to the walls. Meanwhile, Cargo Bays One and Three seemed unaffected. Though Archer at first thought Cargo Bay Two's gravity plating might be responsible, viewing the cargo bay confirmed for him that this wasn't the case. The room was thereafter sealed off. (ENT: "The Xindi")
In the final draft script of "The Xindi", Cargo Bay Two was described as having doors which slid open. In the final version of the episode, though, the cargo bay instead has a hatch which is manually opened.
Shortly thereafter, one of the cargo bays aboard Enterprise was invaded by a pair of Osaarianpirates, who firstly beamed into the cargo bay before one of them used his own particle weapon to knock out a crewman who had been working in the area. The cargo bay was then ransacked by the pair of Osaarians, using small transponder devices. The Osaarians completely emptied Cargo Bay Two and were in Cargo Bay One when they were detected by Captain Archer and LieutenantReed from the vessel's armory, though the Osaarians soon left the ship. Cargo Bay Two was at least partly refilled with the previously stolen cargo once it was recovered from a Delphic Expanse sphere where the Osaarians had stashed it. (ENT: "Anomaly (ENT)")
In the final draft script of "Anomaly", the cargo bay which the Osaarian invaders are shown in, while they knock out a crew member there and ransack the place, was identified as Cargo Bay Two. The designation of this cargo bay is not, however, identified on screen.
Shortly after Captain Archer and T'Pol returned to Enterprise of 2153 following completion of a time-traveling mission to Detroit of 2004, Archer mentioned Cargo Bay Two to T'Pol; he wanted her to ensure that the room be used to store Xindi equipment that, as a result of the mission, was now in the command center on Enterprise. (ENT: "Carpenter Street")
A rare scripted reference to one of Enterprise's cargo bays being called a "cargo hold" was in the final draft script of "Doctor's Orders".
Somewhat worthy of note is a script error in s4e7: "The Forge" where the scene showing the just mentioned 31 human coffins in the cargo bay instead shows 3 rows of 7 coffins totaling 33 human deaths rather than the speech of Captain Archer just prior saying 31 likely a cosmetic choice not intended to be noticed as 31 cannot be easily spread out in an orderly fashion.
The USS Voyager had several bays with the designation "Cargo Bay 2". One had variable environmental controls and was designed for organic storage. It was converted to a hydroponics bay by Kes in 2371 in order to allow for the growth of foods for consumption. Another was located on Deck 4 and suffered a massive hull breach when a Kazon shuttle intentionally collided into it in 2372. In 2374, the Borgassimilated a third "Cargo Bay 2" during an alliance with Voyager. After the alliance, four Borg alcoves remained in the bay and it went back to normal cargo storage. This "Cargo Bay 2", however, was located on Deck 8. (VOY: "Parallax", "Maneuvers", "Scorpion, Part II", "Equinox", "The Gift")
Yet another "Cargo Bay 2" was referenced in VOY: "Night" by Neelix, who proposed the installation of holoemitters to convert the room into a third holodeck; this is assumed to be a different cargo bay than Seven of Nine's, as she would likely object to the conversion of what is essentially her quarters into a public recreation area. The shifting location of Cargo Bay 2 was never explained in dialogue and has never been directly addressed by any member of the production staff. It is presumably simply a mistake made by the writers of those individual scripts, who did not keep up with the location of that particular cargo bay. Alternatively, Voyager was stated several times in the early seasons to have three cargo bays, three transporter rooms, and three holodecks; early drafts of the scripts in question may have referenced the supposed third cargo bay, only to have the reference number corrected in later drafts without also making the location consistent. In any case, the location is most definitively established in VOY: "Scorpion, Part II", which depicts from outside the ship the decompression of cargo bay 2, whose external door is located on what appears to be Deck 7 or Deck 8, on the edge of the saucer section.
Indeed, the confusion of exactly how many cargo bays the USS Voyager has is only complicated by comparing the physical filming model with examples from dialogue. In VOY: "Macrocosm", Janeway clearly says to The Doctor that he has a clear path to "both" cargo bays. Yet, close analysis of the filming model clearly shows a total of three hatches like the one seen in VOY: "Scorpion, Part II" – one on each side of the saucer rim, and a third at the forward tip just below the auxiliary deflector.
According to the VOY Season 2 DVD trivia text version of "The 37's", the Voyager had two cargo bays located on the decks 4 and 10.
The USS Voyager had two cargo bays, one on Deck 4 (Cargo Bay 1) and one on Deck 8. Cargo Bay 2 was in section four, and was used for the storage of spare components and surplus materials. (VOY: "Drone")
At one point in 2377, two deuterium tanks were beamed out of Cargo Bay 2. (VOY: "The Void")
When Nog requested a recommendation from Commander Sisko to enter Starfleet Academy, Sisko decided to test Nog's seriousness by asking him to inventory the contents of Cargo Bay 4. Nog completed the task in a mere five hours, and found items that had been overlooked in the previous inventory. (DS9: "Heart of Stone")
In the final draft script of "Precious Cargo", the Retellian cargo hold was described thus; "Cramped and grungy, dimly-lit. Dented, oily cargo containers fill every available space, and jury-rigged conduits dangle from the bulkheads, where they've been tied into open panels."