Rumble and Laserbeak can be found as hidden cameos in Chapter II: Defend the Ark, and if they are shot at they will retreat. Additionally, Soundwave can be found the same way, but disguised as a Cybertronian light fixture and he will transform, taunt Optimus, and then retreat if the player focuses their aim on him.

In Chapter V: Cut and Run, there is a certain breakable wall that the player can break via Jazz's Grapple ability which leads to a hallway with a switch at the end. If the player attempts to activate said switch it will transform into a robot and proceed to dance. Afterwards, a door behind it will explode revealing a hidden room.

In Chapter XI: Starscream's Betrayal, once you exit outside for the first time, if you travel around the left side of the tower from where you exited, you will come across a small room with an open roof to fall into. The room contains several breakable crates and machinery, alongside a story-related Audio Log from Megatron, but the most unusual thing in the room is a small hologram console that allows you to play a game called "Super Grimlock Quest 64". Pressing the button to start the game will play a short animation and music track featuring still images of Grimlock killing an Insecticon and then getting killed by a giant spider Insecticon, all while Grimlock's health bar depletes in the top-left corner of the hologram screen, suggesting Starscream played the game very poorly.