For those who played the game but didn't watch the anime here's the following differences between the anime & the game.
1.) Virgil died in the Kukai Foundation.
2.) In the anime, Shion has Jr.'s A.G.W.S. & Jr. has Shion's A.G.W.S.
3.) Andrew Cherenkov went MIA after the gnosis attack in Woglinde
4.) Virgil becomes a regular party member until he was killed in the Kukai Foundation.
5.) Shion has no M.W.S.
6.) Shion dive in to KOS-MOS' encephalon inside the Robot Foundation.
7.) The Kirshwasser has a will of its own.
8.) Miyuki wasn't present in the show.
9.) Albedo's A.G.W.S. turn into a gnosis-like creature in the final battle.
10.) Lastly, Jr. knew MOMO before they even met.