Base Modes represent a character when they're untransformed, ordinary people. They're usually Rank E, but occasionally Rank F, and if they're higher than that, something very special is afoot. (For more information, please see: Rank Ranges)
Unlike other Henshin Modes, one's Base Mode is not constructed on the minimum of its Henshin Rank's maximum number of points and a character's master Character Points pool. It is constructed on the minimum number of points for its Henshin Rank. As characters gain more Character Points, they can improve their Base Mode, but only a little bit, with stats and abilities costing four times as many Character Points as normal. This causes a magical girl who begins at Master Rank C, and Base Mode Rank E, to achieve Base Mode Rank D around Master Rank A; once they're at the top of their game (which A represents, on the whole), they're not capable of winning fights while untransformed, but they can at least defend themselves until help arrives. Magical girls who begin above Master Rank C still begin at the bottom of Base Mode Rank E, and will take longer, in the end, to advance to Base Mode Rank D; this is one of many benefits of starting at C.
There is one special way to achieve a Rank D Base Mode at chargen, and it is the most typical way such an elevated base mode rank is gained at all: characters who start entirely without a non-Base Mode, who have sufficient narrative justification for such unpowered ability, may start at a Rank D Base Mode on the condition that they accept a six month minimum delay before they gain any additional Modes. Thus Makoto Kino and Itsuki Myoudouin (both Master Rank C characters, in terms of their overall, post-henshin combat potential) are elbow-dropping Zoisite and Kumojacky while they play their characters well before meeting their true destiny; they aren't remotely in the league of Sailor Mars or Cure Marine, but in the csys they're rewarded for taking the time to develop their characters pre-henshin by getting to keep a Rank D Base Mode after they've earned it by using it exclusively, for the rest of their career. This is always optional; no one is required to do it, and both Makoto and Itsuki are perfectly well-represented with Base Mode Rank E as well, especially if they each invested in a Signature Attack with Master Trait points.
Base Modes have 0 Finisher and 0 Special attack slots by default, and cannot buy more with Character Points; they can only use Free Attacks. A character can, however, buy the Signature Attack ability, granting them a Special available in all of their forms, including their base mode. A classy example of a Signature Attack is Rei Hino's 'Evil, Begone!' banishment with ofuda scrolls; she can use it even when she isn't Sailor Mars, just an 'ordinary' shrine maiden, though it’s backed by less impressive stats and abilities when she does.
While in Base Mode, a character's maximum Fatigue is 20 + (30 for each Rank their Base Mode is above E).
Generally speaking, everyone uses the +transform commands to transform into a Combat Mode before anything else happens in combat. Attacks should never target someone's Base Mode without the defender's consent, though that right is waived if someone starts fighting (including Morale combat and buffs) while still in their Base Mode. Narratively speaking, fighting powered foes in Base Mode is unlikely to have meaningful effect anyway; excessively posing one's Base Mode as being all that effective in magical girl-powered combat is unthemely.
If a character is rendered unable to fight but is still conscious, they should revert to their Base Mode (though they still can't take any combat system-implemented actions).