With the exception of a few minor changes, Transformers: Revenge of the Fallen - Decepticons
plays almost identical to the first movie-based game. The Decepticon/ Autobot branding may seem like a Nintendo-like Red/ Blue branding, but both are entirely different games and allow you to follow your chosen faction through the movie and into battle online.
Every mission features a Story and Challenge mission. In Story missions, you play as a newly arrived Decepticon who is pulled into the faction's quest to recover a fragment of the Allspark. Once you complete three Story missions, the Challenge missions unlock. Here you'll usually play as one of the other Decepticons and complete missions like collecting Energon or fighting off waves of enemies. It's a cool system, but you're forced to complete Challenge missions. Challenge missions live up to their name and can stymie progress. It's an okay idea, but ultimately hurts progression. Challenge missions should be something extra, not something you have to complete.
Multiplayer challenges you to quest-based events and tracks your progress through a leaderboard. These include everything from races to missions where you need to hold off enemies for a specified time period. At the end of the day, the leaderboards are tallied up and the faction with the better score for a particular quest "wins" that quest's region. It's a really neat metagame, but it assumes that equal numbers of players will pick up each system. Currently, the Autobots are crushing the Decepticons, indicating that more Autobot copies are being sold.
Between missions, you can visit the Medical Bay. Here you can increase you base stats using Energon and equip items you uncover during missions. These include stat-boosting items like new parts and weapons. Your created character is persistent across single and multiplayer, so you'll want to uncover all the upgrade parts you can.