Like the console version, the central focus of the two DS versions is a linear campaign of missions, following basically the same story. Additionally, there is an Arena mode with five "arenas", each with six missions available, four bonus levels from the opposing game, and seven multiplayer levels.
Before each mission, you pick two Transformers from your available troops. During the mission, you switch between the two chosen characters using the A button. If a character is knocked out, they can be revived by defeating a certain number of enemies with the remaining character. New characters can be unlocked by completing campaign and arena missions, locating "data disks" which appear as floating golden discs, or using unlock codes. There are thirteen unlockable characters in total, including exclusive characters such as Motormaster, Cyclonus, Grimlock, and Cliffjumper. Other data disks can be selected at the start of a mission to boost character stats.
Characters are classed as "Heavy", "Light" or "Air". While "Air" has the obvious advantage of flight, missions contain areas which only certain classes can go: marked walls can be bashed down by heavy vehicles, and there are small spaces where only light vehicles can go. There are also three weapon types: "plasma" represented by a red circle, "laser" represented by a yellow triangle, and "solid" represented by a blue square. Each character has a ranged weapon (typically plasma or laser) and a melee weapon (typically solid). Enemies are particularly vulnerable to a certain type of damage, which is visible as the symbol representing that damage type above the enemy's head. Advanced enemies can change which damage type they're vulnerable to.
While the foes have health bars that appear over their heads, the player has three bars on their HUD — a health bar, an energy bar, which represents energy they can use to fire, and a boost bar which appears while in vehicle mode, which they can use to boost their speed. All three bars will regenerate in time, though for "Air" characters, the energy bar will not regenerate while they're in vehicle mode.
The game also incorporates a leveling system. Characters begin at level 1 and gain experience by killing enemies and finding energon cubes. Each level gives the character a stat point which can them be spent on one of three stats to increase the character's power. Some stats, when upgraded to a certain level, bestow on the character extra powers, such as new attacks, more powerful weapons, and sundry other abilities. The maximum level possible is 20, giving 19 stat points.
Multiplayer is achieved by using the DS Wi-Fi. Available game types for multiplayer are Deathmatch, King of the Hill, Capture the Flag, and Energon Dash. Additionally, you can play "Ante Games", in which each player bets one of their characters on the outcome. The winner gains the loser's ante character, but the loser can unlock their character again by playing a "rescue" mission, assaulting a prison to free the lost character. Data disks which are exclusive to certain levels available only in the opposite version can be obtained only by playing in multiplayer.
Mission 1: The Plot Forms
Ironhide and Ratchet have discovered that Megatron seems to be searching for something at a training facility, so Ironhide sends an Autobot rookie there to investigate. Once he arrives, Air Raid gives him some basic training. Training is interrupted with the news that the Decepticons have taken the control room, and Air Raid goes to help. The rookie is sent to get some data links back online, which he does, facing some laser guards into the bargain. Unfortunately this is followed by Megatron bursting through a wall and blasting him. Megatron is contacted by Soundwave, who's hacked into the Autobot mainframe, but needs a diversion to give him time to decrypt the data. Megatron rendezvous with a Decepticon dropship, which drops off Dirge and another Decepticon. The trio move into the facility, destroying as much as they can. The third Decepticon is attacked and destroyed by a swarm, and a short time later Megatron is taken out by a laser guard, but with Brawl's help, the Decepticon leader is back on his feet in no time. Finally Soundwave reports he's completed his mission, and Megatron's team heads for the extraction point in vehicle mode. They haven't gone far when they run into Jetfire, who blasts Dirge out of the room and battles Megatron. One short fight later, and Megatron receives a report from Soundwave that he's found the location of the Trypticon Space Station. Megatron orders his ship readied.
Mission 2: Reviving the Dark Energon Project
Megatron takes his ship to the space station, but the inhabitants take up defensive positions, and Barricade reports the shields are down to 15%. Megatron's prepared to ram the ship into the station, but the debris field prevents them getting any close. A team of Decepticons is dropped off and jumps between chunks of debris until they reach the station itself. Starscream meets them at the door, announcing he's not going to allow them to reactivate the base and, activating the emergency defense systems, runs inside. The Decepticon team fight their way inside and forcibly shut down the defenses, then reroute the power flow to feed back into the core. This done, they head for the lab to restart the Dark Energon project, however standing in their way is Starscream. Though the air commander fights well, he's defeated and begs for mercy. Megatron allows him to join the Decepticon cause, and Starscream opens the lab, reactivating the Dark Energon project. Soundwave suggests they test the Dark Energon somewhere safe, so Megatron opts to do so at back at Kaon.
Mission 3: Testing the Experiment
- Unlockable character: Thundercracker
There's the chance that the Dark Energon use will result in fatality, so Barricade has set up Kaon Prison as an assault course, and several of the Decepticons are imbued with the substance. In addition to the swarm infesting the facility, some of the Autobot prisoners have been deployed to add extra combat. The Decepticons make their way down a treacherous winding catwalk in a tower and through ventilation ducts, before testing their navigation skills on an underground area mined with depth charges. Eventually they reach stage 2 of the test, and must fight their way through corridors to the combat arena. Though the opponents gets steadily harder, the Decepticon team reaches the arena, where Barricade reveals the final test — one-on-one combat against Ironhide. They manage to defeat the Autobot, however the test have depleted almost all of Trypticon's reserves of Dark Energon. Megatron orders Starscream to find a way to make more while he goes and sits in his war room. Soundwave prepares to infuse a reluctant Barricade with Dark Energon.
Mission 4: Reactivating the Energon Bridge
- Unlockable character: Onslaught
Starscream's deciphering of some ancient data files reveals the existence of a geosynchronous space bridge hidden in Cybertron's core, used by the Ancients to channel power to the Trypticon station. Starscream sets up a computer station to monitor the progress of the Decepticon as they head into a hostile area of Cybertron to locate the access gate. They reach what appear to be canals with no direct path through, but they manage to make their way across despite the swarms and deadly wall turrets which attack them. Beyond they find a fork — they have a choice between a path tricky to navigate versus a path with a lot more enemies to fight. They pick a path and eventually find themselves two sectors from the gate to the core of Cybertron. The next two doors fall in short time, and they reach the control room, allowing them to open the access gate to the core and step inside. Soundwave warns the team that their presence has reactivated long-dormant defense systems. Starscream believes he can find a way inside.
Mission 5: Activating the Uplink
The Decepticons have reached the geosynchronous energon bridge causeway. Soundwave reports that Trypticon's power cells are exhausted and the supplies of Dark Energon are at 20%. Starscream has worked out a path that bypasses most of the threat. The Decepticon assault team heads along a corridor and takes a short cut through a room filled with superheated gases which they must rush through in vehicle mode to avoid damage. Following huge pipes, they fight some more turrets, and past a room crackling with energy, they breach a series of force fields with conspicuously-placed controls. They eventually reach a control room from where they successfully reroute the power into the energon bridge. They head for the bridge itself to manually connect it to Trypticon station, however their imminent victory is interrupted by Silverbolt, who sets up energon suppressors and sics some Autobots on the Decepticon team. The Decepticons make short work of the protectors and destroy the suppressors, however the interference means they have to reroute the power using the back-up link. In the control room for the back-up link, they encounter Silverbolt himself and trounce the Autobot before achieving their goal. To the Decepticons' collective surprise, the new link only repowers Trypticon to 37%—the Autobots have severed the link to Cybertron's core using Omega Key encrypted locks. Megatron orders Soundwave to assemble a strike force to find said key.
Mission 6: The Attack of Iacon
- Unlockable character: Dragstrip
Laserbeak intercepts a transmission in which Zeta Prime tells Optimus to protect the library while he secures the key. Megatron orders a strike team to Iacon to retrieve the key. The Decepticon team breaks through a force field on the outskirts of Iacon and blasts their way through the initial resistance, before passing a huge lake of Energon. Beyond, they find ruins protected by turrets and a few hapless Autobots. After blasting through the ruins, they pass through an old beaming facility and into another building where they find and dispose of an Autobot ambush. They locate the pylon which regulates Iacon's power and re-energize it, allowing them passage through a room in which the power is channeled. After meeting some more Autobot resistance with lethal force, they reach the main part of the repository. Starscream tactlessly points out that the information they've gathered is encrypted, and on their way in, they've just wiped out the Autobots who could decrypt it. Megatron tells him to shut his mouth.
Mission 7: The Omega Key
- Unlockable character: Dirge
Starscream breaks the encryption and finds the Omega Key is being held in the heart of Iacon, but is skeptical that Megatron will succeed in getting hold of it. Heading out of the building, they cross a broken bridge and blast their way in to the next tower. A door proves particularly troublesome when unlocking it unleashes a mess of swarms and depth charges, but they manage to shoot their way through and breach Iacon's perimeter defenses and start heading for the Iacon Library. Down a corridor heavily infested with turrets, they take out another Autobot, and reach the Stellar Galleries. The galleries are lightly defended, but outside they encounter more Autobots at the entrance to the library. Without stopping to admire the library's grand architecture, they hunt for Zeta Prime. A bit of shooting later and they find a vaulted area with a heavy security field and the Omega Key behind a force field. Though they deactivate the force field, the door closes before they can take the key, and Zeta Prime reveals himself! Safe behind his force field, he shoots at the Decepticons, but they're able to deactivate the force field and blast him. Zeta Prime refuses to turn over the key, so Megatron slags him, takes the key, and uses it. Zeta then informs him that that key only activates the real key to the core, which will shortly come to him. Omega Supreme has been activated and with a might blow, quickly takes out most of the Decepticons in Iacon. His next objective: destroy Megatron!
Mission 8: Omega Supreme
- Unlockable character: Soundwave
Though the other Decepticons are ready to retreat, Megatron tells them to stand firm and accuses Starscream of planning this. Starscream taunts him in return, but claims he can still restart the link between the core and Trypticon station. Megatron orders the attack. Cliffjumper spots them incoming and sets a bunch of mooks onto them. The Decepticons mow through them and break into the building, so Cliffjumper sets up a force field to slow them down. They manage to bypass it and pursue Cliffjumper down long corridors, exchanging fire. The chase ends when Cliffjumper crashes into a wall and feebly protests as the Decepticons run past. They next encounter Jetfire who's surprised they got past Cliffjumper, and sets more Autobots onto them. The Decepticons fight their way through the resistance and chase Jetfire down a bunch of corridors, before he ditches them in a room overrun with swarms. After some pest control, the Decepticons manage to get through the door and follow Jetfire, only for him to turn the base's full defenses on them. Another chase ensues, and they finally corner and finish off Jetfire. As they race through the corridors, Omega Supreme's claw punches through the wall and they finally face him. The other Decepticons hesitate, but Megatron gives a rousing speech and they raise the courage to attack Omega. When the titan finally falls, Megatron announces that the infusion is complete, Cybertron is his, and the Autobots are a broken army. All hail Lord Megatron!
Mission 1: Gathering troops
Zeta Prime makes a distress call which surprises the Autobots, as they thought he'd bought the farm. Optimus isn't available to take his call, and he's cut off before he can tell Ironhide where he is. The Decepticons have cut the data links to prevent further communication. The Autobots send Bumblebee to find Optimus. Ironhide sends a rookie to help Ratchet and Air Raid. They've barely finished some basic training when news comes that the Decepticons have taken the control room, and Air Raid leaves to help. The rookie goes and gets the data links back online. He's only just informed Ironhide of the fact when Starscream bursts in, ready to terminate him. Luckily Optimus crashes through a nearby wall, and Starscream flees. Optimus heads into the facility proper, and runs into reinforcements in the form of Jetfire and another Autobot. As they move through the facility, the third Autobot is destroyed by a swarm, and then Optimus is taken out by a laser guard. With Bumblebee's help, Optimus recovers and they head for sector 5, where Ironhide has detected Decepticon activity. A not-so-leisurely drive later and they come face-to-face with Dirge, who promptly gets his skidplate kicked. The data links are back online, but Optimus reminds everyone that they must retake Iacon.
Mission 2: Retaking Iacon
Jetfire reports that the Decepticons' Dark Energon corruptors are causing major damage to Iacon and the Decagon defense grid. The corruptors must be destroyed to restore contact with Zeta Prime. Optimus reminds everyone that he's not the leader and is intending to return to the docks once the war is over. The Autobots head into Iacon, destroying the turrets and Decepticon in an energon channeling plant. They find a lake of Dark Energon, which Ironhide warns would be hazardous to fall into (no, really?!) and manage to get across. The walls here are encrusted with Dark Energon crystals and beyond they find a Dark Energon corruptor. The Autobots destroy it by taking out the spikes, but Ironhide reveals there are two more of the things near the Decagon. They continue on until they reach the entrance to the Decagon, and, after destroying the two corruptors, they head inside and reactivate the defenses. All that's left to do is wait for Zeta Prime to make contact again.
Mission 3: Infiltration of Kaon
- Unlockable character: Cliffjumper
With the DataNet back up and running, Zeta Prime manages to contact the Autobots to let them know he's being held prisoner in Kaon Prison. The Autobots send a team out to rescue him. They first work their way through a security sector to the prison entrance. Though the main gate is sealed, they activate a bridge and are able to break in via a secondary entrance. Within, they must first navigate an underground area heavily mined with depth charges and hazardous Dark Energon pools. After a brief crawl through ventilation ducts, they traverse a winding catwalk in a tower to the upper prison levels, destroying the generators to the force field protecting it as they go. Once they reach the prison control room, they're able to gain access to the next area, leading to the central processing station. As the door's magnetically shielded, they take out the generators powering it. They unlock the door but are confronted by Onslaught, who's determined to protect the station at all costs. After a vigorous battle, the Autobots head into the station, though Bumblebee is sure it's a trap.
Mission 4: Rescuing Zeta Prime
- Unlockable character: Sideswipe
Jetfire reports that Zeta Prime is being held in a nearby cell block. Ironhide's keen to bash more Decepticons, but Optimus reminds him of their mission. Megatron is amused by the rag-tag team which has come to rescue Zeta, and orders the Decepticons to destroy the invaders. Crossing a fast-flowing river of Dark Energon, the Autobots encounter a boastful Decepticon guard who sets a few tanks on them. When the Autobots easily destroy those, the Decepticon faces them himself, and is likewise dispatched. They continue on, over another bridge and fight their way through more Decepticons until they reach the cell block. One of the prison wardens promptly unleashes the mysteriously fully-armed prisoners on them. When that doesn't work, he attacks them along with some grenade turrets, but fares about as well as the prisoners. The Autobots continue through an area with pedestals they have to hop across to reach another door, beyond which is another cell block. The prisoners there are released as well. Once they're dealt with, the Autobots cross another massive bridge and finally find Zeta Prime. Zeta is mortally injured, and Optimus returns his body to the High Council. The High Council make Optimus the new Prime, and task him with curing Cybertron's core of its Dark Energon infection.
Mission 5: Gaining strength
- Unlockable character: Swoop
Optimus approaches Grimlock and Swoop, but Grimlock's not interested in fights with Decepticons. Though talks quickly break down, the Autobots use psychology and Grimlock agrees to join them if Optimus can prove his strength against Grimlock. While they're talking, the Decepticons abduct Swoop, and Grimlock asks the Autobots to mount a rescue. The Autobots head to the outskirts of Iacon and break through a series of force fields. A couple of Decepticon defenders trap them in another force field for an impromptu cage match, but aren't much of a challenge, however in the next room they encounter the mighty Cyclonus! Safe behind his force field, Cyclonus sets some "minions" on them, but when the minions are defeated and the force field disabled, Cyclonus feebly lets them past. They find Swoop in a lab, attached to some sort of device. When they free him, they find he's been experimented on with Dark Energon, and is out of his mind. By jolting him with the other machinery in the lab, they purge him of the infection and he says he'll repay them by showing them the quick way out. Unfortunately, Cyclonus has rigged the lab to blow in one minute, so Swoop and the Autobots have to quickly travel down a series of corridors, disabling force fields as they go, in order to escape in time. Grateful, Grimlock lets Swoop join the Autobots, and will tag along for the time being to protect Swoop.
Mission 6: Saving the core
Having obtained core samples, Jetfire and Ratchet have determined that the only thing stopping the core from healing is the corruptors. The Autobots therefore head for the core. After battling a Decepticon captain, they traverse another corridor full of Decepticons, and bypass another force field, then find themselves following a set of massive pipes, until they come to a room filled with superheated air, which they speed through in vehicle mode to minimize damage. More fighting ensues and then the Autobots must breach another force field while avoiding floor-based hazards. They reach an area rich in Dark Energon, which Optimus reasons is where the corruptors will be. After battling some more Decepticons, they take out the power supply to the corruptors, and are confronted by Brawl. Brawl boasts that he himself will supply the backup power, and engages the Autobots in battle while displaying the unique ability to spawn swarms. The Autobots defeat him, saving the core. The core, however, is unable to sustain them while it recovers, so Optimus says they must leave in ships. They have one last thing to do, however: destroy Trypticon Space Station.
Mission 7: Destroying Trypticon space station
- Unlockable character: Warpath
Trypticon station is closing in on Cybertron, destroying the fleeing Autobot ships as it goes. Optimus orders a strike team to ascend the space bridge to Trypticon. Ironhide protests that it's suicide, but Optimus is determined to protect the Matrix of Leadership and the future of their race. They get on board Trypticon and head for the main energon pumps. The place is swarming with Decepticons, and more come running when the pumps are disengaged, but the Autobots continue on. The intense fighting causes a power surge, knocking out the station's primary systems. The Autobots get the energy flowing again, but that just attracts more Decepticons. After a while smashing Decepticons, one manages to ambush them at a bridge, but it doesn't slow them down long. Unfortunately the power goes out again, and Ironhide determines something's causing a serious power drain. As the station quakes around them, the Autobots find Trypticon's main cannon. They destroy the cannon and, with the power core destroyed, there's now nothing keeping the station in orbit (except, y'know, basic physics). The Autobots flee at full speed through the collapsing station and make it out in time. Their relief is short-lived, as the station itself is transforming! Grimlock thinks it looks familiar.
Mission 8: Trypticon
- Unlockable character: Jetfire
Optimus rallies his men to make an assault on Trypticon. They first encounter a couple of corruptors disrupting power, which they take out along with their Decepticon guards. Further along they run into Ironhide, who's pinned down and can't reach a security access panel. That problem is solved by the application of some gunfire. The Autobots blast their way through more resistance, including a group of melee specialists who mob them. Getting closer to the crash site, the Autobots pass through more hazardous areas filled with superheated air, eventually reaching an area filthy with Dark Energon. They fight a few more Decepticon mooks before finally reaching Trypticon himself. The beast is huge, and they fight him from a bridge until he destroys the platform with one swipe of his tail. They keep pounding at him, and finally Trypticon falls, defeated. Optimus gives a last rousing speech declaring they will keep Cybertron alive in their memories forever and the Autobots flee Cybertron in their ships.
- Optimus Prime
- Ultra Magnus
- Air Raid
- Autobot rookie