While she's "at rest", as Miss Martian says, she resembles a giant red and black egg. When she "wakes it", she becomes a large aerodynamic ship. This shape-shifting also allows her to morph into other forms, including that of an SUV and a Recreational Vehicle.
The Bio-Ship is capable of going into space, withstand the friction of a rapid descent, and endure the shockwave of a nuclear explosion. It can also function as a submarine.
She can turn near-invisible in camouflage mode. As stated above she has shape-shifting ability, allowing her to adapt to the user's needs, such as move from her at-rest form to flight mode, to create or remove seats as required, to open hatches in her outer hull, and to generate a clamp capable of holding a large aircraft. She is also theoretically capable of assimilating alien technology.
The Bio-Ship has offensive capabilities, such as a ray gun in the gap between the nose and laser cannons on its sides. Nevertheless, she can also incorporate external weaponry, but her innate weapon systems need to be off-line during the process. She is also equipped with Darkwear interface.
She is not invulnerable to damage, and afterwards it may need a short period of recovery. She can psychically shield to her passengers but this can be overwhelmed.
During the Team's disastrous telepathic training exercise they flew to Superman's Fortress of Solitude to take out an alien ship. Miss Martian upgraded the weapons systems with alien technology, but the ship was lost during the destruction of Washington, D.C..
Miss Martian and Superboy had used the ship to travel to Qurac to visit the Logans. The planned to use it for a trip to Dhabar later; in the meantime, it hovered, cloaked, over the sanctuary grounds.
Qurac December 1, 10:31UTC+2
M'gann and Conner left the sanctuary in the Bio-Ship.
The Bio-Ship continued on towards the Moon. Miss Martian was concerned they wouldn't make it in time.
The Moon December 1, post-19:36UST
The Bio-Ship picked up the missing heroes's signals on a ship moving away from the Moon. They pursued the ship, though M'gann noted the alien vessel had a head start and the Bio-Ship could not follow if it went to light speed.
Before M'gann and La'gaan could share a kiss, the Bio-Ship alerted an object at close proximity of their ship.
Kylstar's Vessel December 1, 23:17UTC
The Bio-Ship moored underneath Kylstar's Vessel. As there was no airlock, Lagoon Boy remained at the helm.
Kylstar's Vessel December 1, 23:58UTC
Having decided to release his prisoners, Kylstar had all those who wished to leave teleported home, including Lagoon Boy and the Bio-Ship.
The Collector's Ship December 1, 19:01EST
Those taken from Earth were teleported inside the Collector of Worlds's ship, where other members of the League and the Team were battling the vessel's commander. After Nightwing ordered them to join the fight, La'gaan destroyed the Collector with the Bio-Ship's weapons.
Metropolis December 1, 19:03EST
La'gaan landed the Bio-Ship and exited, as dozens more coludroids appeared. However, the Collector having detected that someone on the surface was about to shut down his probe, and surprised by the survival of a Kryptonian, agrees not to preserve Metropolis.
The Team and the League used the Bio-Ship to travel to Malina Island, with Nightwing at the helm. They dropped off Aquaman and Lagoon Boy first, and then Batman and his protégé's disembarked. Martian Manhunter and Miss Martian, who had been on the island undercover, escaped the Krolotean base and picked up the others. As a powerful bomb had been planted and primed on the island, they had to retreat quickly. The Bio-Ship couldn't outrun the blast, but could withstand its outer edges, though barely.
Miss Martian summoned the Bio-Ship to save a falling plane that was heading off a ravine. The plane, with Batgirl and several kidnapped children aboard, had its wings clipped off, and was too heavy for Wonder Girl and Miss Martian. The Bio-Ship produced a large clamp from its hull, and carried the fuselage to safety.
Miss Martian and Superboy used the Bio-Ship to patrol the skies to protect the launch of Ferris Aircraft's Earth-Mars communication satellite. After Lagoon Boy found their enemy under water, Miss Martian left and Superboy used the Bio-Ship to destroy several missiles Kaldur'ahm fired at the rocket.
With the Bio-Ship in camouflage mode, Nightwing, Miss Martian and Wonder Girl followed the Manta-Flyer carrying Alpha squad from Star City docks to a Reach vessel in the Pacific Ocean. Miss Martian left to infiltrate the ship.
After Superboy secured the Reach ship's docking bay, the Bio-Ship docked with the alien vessel. Numerous captives on the Reach ship were evacuated to the Bio-Ship, but Black Beetle sealed the docking bay doors, trapping Nightwing in the Bio-Ship and keeping the rest of the Team out. Blue Beetle later arrived to open the doors, and everyone but him was able to get aboard before the Reach ship's hull was breached. Both the docking bay and the Bio-Ship began to flood, forcing Nightwing to seal the Bio-Ship's hatch. The Bio-Ship undocked and, dodging the Reach ship's weapons fire, deployed Lagoon Boy to rescue Blue Beetle, who had been blown into the ocean during his battle with Black Beetle. The Bio-Ship picked the pair up and sped away from the scene.
Camouflaged, the Bio-Ship deposited most of the Team aboard the Warworld. Afterwards, Batgirl and Robin used the Bio-Ship to provide cover fire for the League members attacking the Warworld's surface.
The Warworld May 26 post-12:35, UTCTime Zone
As Mongul launched a saturation missile attack on Earth, the Bio-Ship and the Leaguers attempted to destroy as many missiles as possible. Batgirl reported to the Watchtower that the Bio-Ship estimated their efforts would take out 64% of the missiles.
The Warworld May 26, post-12:40UTC
After the Team members infiltrating the Warworld succeeded in shutting it down, the Bio-Ship docked at the entry point, and the Team reunited.
Nightwing and Miss Martian used the Bio-Ship to search for the Team. The Warworld's size meant they could not effectively scan the entire ship from outside, so they decided to return to the docking bay.
There, they were reunited with Sphere and went on to successfully locate the already liberated Team, at which point they all retreated to the Bio-Ship.
Bio-Ship carried M'gann, Aqualad, Nightwing, Artemis and Blue Beetle to the site of a belatedly detected MFD. They landed and disembarked to watch as Flash, Kid Flash and Impulse successfully shut it down, but were dismayed to find their victory was at the cost of Kid Flash's life.