Lost Memories saw the introduction of two new game features:
- Memory Crystals II allowed characters in Events the option of breaking a second level cap at level 65 after first breaking the initial level cap at level 50, allowing the featured character(s) to improve stats and Synergy as they fight. The level limit has been raised to 80. Cloud would be the first unit to receive a Memory Crystal II.
- Super Soul Breaks and Soul Break Mastery: In a Relic Draw, characters now had a chance at acquiring rare equipment with more powerful Soul Break moves. Soul Breaks can be learnt and mastered at will, allowing players to carry their unique skills without the Soul Break equipment having to be worn at all times; and Super Soul Breaks, when mastered, also augment the target character's strongest stat permanently. When a character acquires any Unique Soul Break, that character's weapon or armor with the move on it gets its own Mastery gauge, which fills in proportion to earned EXP and can be assisted by Synergy. Cloud had an opportunity to acquire Blade Beam from the sword Organics (VII), which in turn augments his Attack by 10 points when the move is mastered.
This was also the game's first attempt at a quick-play event, as each half offered only five dungeons at a time until Bonus Battles were added to the second half. One or more Bonus Battles would then offer the Memory Crystal II. This format would become the default for all events from mid-2016 forward, when the Bonus Battles also became permanent.
Unlike the previous two continuous events, Lost Memories ran on two tracks set at different points in time.
The "Rescue" track featured select events from the AVALANCHE bombing raids on the mako reactors to the party's eventual escape from Midgar. The event then shifted to the "Pursuit" track as the party attempted to follow the trail laid by Sephiroth in his own quest to conquer Gaia.