Quests are optional missions in PSO that give rewards for clearing them. Ephinea offers both the original Sonic Team quests and an assortment of community- and staff-created quests. The majority of quests are available to play in both One Person and multiplayer mode, but some are specific to one or the other. Quests are started at the quest counter, and displayed by category, along with a short description for each quest. Quests are cleared in various ways, with some not having any clear condition at all; most of the Shop quests fall into this category.
The Government Quest counter is located in the Principal's Office in Episodes 1 and 4, and in the Lab in Episode 2. Similar to previous versions of Phantasy Star Online's offline story missions, Government Quests involve investigating the surface of Ragol and moving through the main story of PSO. Government Quest unlocks are episode-based, so clearing Episode 1's quests isn't necessary to play Episode 2 or 4's quests. Additionally, some Government Quests give out rewards the first time they're cleared on a given character and difficulty. Unlike other quests, players may join Government Quests while they are in progress.
The Hunter's Guild counter is located on Pioneer 2, in the same room where players initially spawn. The Hunter's Guild contains all non-Government Quests. In multiplayer, it consists of five subsections: Extermination, Maximum Attack, Retrieval, Shop, and VR. In One Person mode, the Hunter's Guild contains two additional subsections: Side Story and Solo Only. Rewards for completing missions differ depending on the content of the mission. The Hunter's Guild counter is also used to begin Battle and Challenge Mode games.
Challenge Mode stages are available for both Episode I and II, with each Episode having 9 and 5 stages respectively. To play Challenge Mode, it must be selected during party creation in the lobby. Parties must clear stages sequentially in order to progress. At the start of each Challenge stage, all levels, equipment, and learned techniques will be reset to the stage's default. Returning to Pioneer 2 is not possible until a stage is either failed or cleared. Each player is given a set number of Scape Dolls; these are the only way party members can be revived. The whole team will be sent back to the Hunter's Guild if the HP of one of the participating member drops to zero and they have run out of Scape Dolls.
In Battle Mode, players battle one another by rules set by the party leader. To play Battle Mode, it must be selected during party creation in the lobby. At the beginning of each game, the rules set by the team leader will be displayed; each player will be positioned at one of four starting locations. Players compete to defeat as many of their opponents as possible within the time limit. Certain weapons, items, equipment, Mags, and techniques may be unusable, depending on the selected rules. A player falls when their HP drops to 0, and the fallen player will respawn at a random location on the map. The game is over when time expires.