.Shortly after the end of the previous game, Edward and Alphonse return to Resembool to fix Ed's automail and check on Winry. However, they are disturbed by a strange group that pursues someone. After driving the group away, Ed and Al learn that the stranger is a rogue member of Liberale, a terrorist organization, responsible for several bombings. Before dying, the stranger tells them that Liberale's next target is military HQ in East City. The brothers move out to alert the HQ, and Winry decides to tag along with them.
The game contains examples of:
- Abnormal Ammo: Winry uses an alchemic gun, so all of her "alchemy" attacks take the form of this trope.
- Action Girl: Winry, of all people, was upgraded to one. While underwhelming at first, after getting the alchemic gun, she becomes the second most powerful party member. The newcomer Viola is also no slouch in battle.
- Almost Dead Guy: The guy at the start of the game is mortally wounded by Liberale members, and lives long enough to namedrop the organization and tell the party about their next target.
- Battle Strip: In addition to the usual Ed's and Armstrong's The Coats Are Off, Winry takes off the top part of her overalls before every battle.
- Big Bad Friend: The big bad, Lute, spends some time in your party, and no one really suspects him.
- Bomb-Throwing Anarchists: Liberale is a terrorist organization, that arranges bombings and stirs up prison riots. Their name, meanwhile, tells that they ostensibly fight for liberty. Subverted after all, as their motive is not a political one. In truth, Liberale is a group of sentient chimeras, who want to take revenge on humanity.
- Call-Back: There's a couple of references to the previous game.
- A certain healing alchemist, all but stated to be Corniche Royce, is said to be the one who healed Viola before the final battle.
- The Big Bad of the first game, Lincor, with his bioalchemy abilities, was a part of the current Big Bad's plan to restore his lover Lila. Naturally, the former's death threw a wrench into this plan.
- Canon Foreigner: Two party members, Viola Amore and Lute Zaxophone, as well as a major NPC Cravis Fagott, were created specifically for the game.
- Cognizant Limbs: The final boss is composed of the big bad, fused with a wall, and two apparitions of his Lost Lenore that heal and support the main body.
- Combatant Cooldown System: The combat system is unchanged from the past game. Before the player can order characters to act, their gauge must fill up. Skills additionally require some charge time, while normal attacks and items are used right away.
- Combos: When two or three attacks are made one next to the other, the background will change to blue Speed Stripes, and the following attacks will deal more damage than usual. Normal attacks can be chained into skills, but not vice versa. Additionally, there is a chance, affected by Relationship Values, that a party member will make a follow-up attack, which will change the color of said Speed Stripes to red.
- Death Dealer: Lute fights with a deck of cards, and even flips through them in one of his combat animations.
- Evil Makeover: Big Bad pre-reveal: neat and sane. Big Bad post-reveal: disheveled and constantly grimacing.
- Healing Shiv: Winry's alchemic gun has several moves that heal the party, usually with some added bonus, like an increase in a certain stat.
- In the Hood: All Liberale members wear cloaks with hoods, that completely obscure their faces. It serves to hide the fact that the leadership of Liberale are in fact sentient chimeras.
- Lazy Backup: You have up to four people in the reserve, and they still won't help you if the party is KO'd.
- Love Makes You Evil: The Big Bad's motivation. Some time ago, he was forced to turn his lover, Lila, into a chimera, and since then he tries to create Philosopher's Stone to restore her. That includes killing people to make the Stone from their blood.
- Non-Lethal K.O.: The only thing that depleted HP does to party members is turning them gray and putting them into "wounded" animation. They will still move along the rest of the party on the battlefield. Thankfully, they don't require specific "raise" items, and can be revived with any healing.
- Obvious Rule Patch: This time around, Ed's alchemy skills require substantial time to charge, making his slightly less broken than in the previous game.
- Outside-the-Box Tactic: Scar evades every alchemy attack, and hits hard enough to make battling him with normal attacks unviable. The solution? Use "Mind-eye Strike", a consumable that guarantees landing a hit!
- Point-and-Click Map: That's how railway is depicted here.
- Relationship Values: If two party members fight alongside each other long enough, their friendship will strengthen, and they will get a higher chance to make a follow-up attack in a combo.
- Status Effects:
- Damage-over-time Poison, action-preventing Confusion, skill-blocking Dumbness and hit rate-lowering Blindness. These are shown in bubbles alongside the character.
- There are also stat changes, in which the entire sprite of the affected character will blink with a color. Red is attack, blue is defence, green is speed, and yellow is evasion. Fast blinking means a decrease in the stat, and slow blinking means an increase.
- Spontaneous Weapon Creation: Just like in the previous game, Ed can use alchemy to create weapons from surrounding materials. It's presented as a set of five cards, that the player can either use right away, or combine in certain ways to make better materials with stronger attacks.
- Super Move Portrait Attack: The game ditches animated inserts from the previous game, and goes for traditional portraits before executing any skill.
- Universal Poison: Poison still can damage Alphonse, even though he's a suit of armor with a bound soul.
- Wrench Wench: Viola is an automail engineer, and all of her attacks are themed around various instruments. She and Winry actually bond over their shared profession.
