The desired effect may just be too complicated…

The first spell commonly available to move a foe to another plane is, in fact, the 5th-level cleric spell mudança de avião [conj] (Manual do Jogador 262). Its low level compared to the sorcerer/wizard version means that a high-level cleric can prepare several such spells—enough, anyway, for an infiltration mission during which foes are to be dispatched to other dimensions yet not—deliberately nor technically—outright killed.

Usando o feitiço mudança de avião in such a fashion still carries with it some risk: if the caster says, "I mudança de avião the guard to Mechanus," for example, ou the spell fails because Mechanus is no more a destination than the Material Plane or the DM randomly determines where on Mechanus the poor guard ends up. This is less of an issue if the cleric faz have a destination in mind ("Because everybody loves the Cidade de Brass, right?"), but the subject will ainda be from 5 to 500 miles away de that destination, which could be fatal if the destination is on, for instance, the Elemental Plane of Fire.

(A unique case is when a creature's sent to the Seven Mounting Heavens of Celestia: folks sent to aquele plane always end up on the shores of the lake surrounding the base of Mount Celestia, and probably near an inquisitive angel bear. I wish I were kidding.)

O feitiço de clérigo de nível XIXUMX maior deslocamento de avião [conj] (Compêndio de Feitiços 159) solves the off-target issue, but the caster must've once visited the destination, and the spell's higher level means devoting even greater resources to multiple castings.

Enough gold solves at least some of volume problem, though. If the caster can modify the spell plane shift et al. with the metamagic feat Alcance o feitiço (Divino Completo 84)—it's level adjustment is usually +2 but ways to mitigate that exist—, the caster can employ an expensive haste metamagica of chaining (Compêndio de Item Mágico 164) and, possibly, disappear all at once a bunch of guards (if they possess not-very-good Willpower saving throw bonuses, anyway).

Keep in mind, though, that spells like mudança de avião typically don't enable the subject to retorno to its starting plane. Once the subject's affected, the subject's on its own on that new plane, and that might as well be a death sentence (or at least a triste sentence) if, for instance, the subject's a generic level 4 human warrior or whatever.

Outros efeitos pode do similar things. A trap could be set by a high-level caster using the 4th-level Sor/Wiz spell desert diversion [conj] (Sandstorm 113-4) on the infiltrator's próprio high-level method of entry into the facility, for instance, and such a portal'll briefly zap away investigators to a distant wasteland, but that's sloppy and unreliable without another spell like the 8th-level Sor/Wiz spell simpatia [ench] (PH 292) or something. And the 8th-level Sor/Wiz spell labirinto [conj] (PH 252) does just about exactly what you want, but, it, too, uses an 8th-level spell to avoid killing folks, making it, frankly, excessive.

…How about something simpler?

Ideally, the infiltrator'd use the 3rd-level psion/wilder power salto no tempo [psychoportation] (Manual Psiônico Expandido 137), but, unfortunately, psionics are unavailable. However, the existence of an effect like salto no tempo raises the possibility of a traditional caster researching a similar original spell (DMG 198). There are, after all, mechanics for such an effect already.

But let's keep in mind the goal: make guards temporarily unaware of actions taking place around them in a nonviolent fashion so that they can't testify as to what the infiltrator did. May I suggest the humble, reliable, 40-year-old 1st-level Sor/Wiz spell dormir [ench] (PH 280)? And it's big brother, the 3rd-level Sor/Wiz spell sono profundo [ench] (PH 217)? Combined with the 4th-level Sor/Wiz spell maior invisibilidade [illus] (PH 245), the caster should be able to get near enough to use these spells and render the victims insensate so that the caster can go about his task undisturbed, and the victims'll awaken undamaged, hopefully (if the caster's quick enough) after the caster's departure. The metamagic feat Feitiço Silencioso (PH 100) and the 2nd-level cleric spell silêncio [illus] (PH 279) may be of use to the infiltrator, and the object upon which the silêncio spell's cast could even be [cue dramatic music] a clue!

Such a workaround also eliminates the need for the caster to create a demiplane that erases memories (an unlikely prospect anyway as memory isn't a planar trait that can be specified even with a generous reading of the 9th-level spell gênese).

Your proposal sounds feasible within the RAW, it sounds like the Plane Shift spell would be what you need. The spell does allow a save when the target isn't willing.

As it is a fairly high level spell, the target 'knowing' exactly what happened could certainly be very nebulous. If they were conscious, they probably know that someone seemed to cast a spell on them. If they were sleeping when the spell was cast on them, they might just wake up somewhere different.

Genesis is a good choice for a spell, it's very similar to 5e's Demiplane spell. As such, if you create the plane it's reasonable for the creator to know exactly how to make a unique tuning fork for the Plane Shift spell's focus.

If your story allows for your antagonist to work with assistance, he might have an ally that casts Modify Memory as well (http://www.d20srd.org/srd/spells/modifyMemory.htm) to remove any memory of the casting. If your BBG's only goal is for people to not remember his deeds, then this might be the only spell you need. Otherwise, he might need an assistant to cast this spell in addition to Genesis and Plane Shift (assuming he's a powerful cleric or wizard).