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Waypoints, or Vortex Waypoints, were points in time and space that became supercharged with vortex energy.
During a temporal crisis which grounded TARDISes and similar machines throughout the universe, the Doctors realised they could only travel from one Waypoint to the next, draining each of vortex energy to temporarily, messily re-power their TARDIS before depleting their reserves with the next hop. (GAME: Lost in Time)
Temporal incidents and vessels
Due to the confluence of TARDISes, or vortex-related objects both Diner TARDIS where Clara Oswald parted ways with the Twelfth Doctor, and Atlantis caught in its final moments in a time eddy) because of the [[Crystal of Kronos] had become charged with energy. (TV: Hell Bent [+]Loading...["Hell Bent (TV story)"], The Time Monster [+]Loading...["The Time Monster (TV story)"], GAME {[cs|Lost in Time (video game)}})
Likewise the Underhenge right before the Eleventh Doctor was placed in the Pandorica was also a temporal focal point. (TV: The Pandorica Opens)
The Dalek City on Skaro at an early point in its history had become charged with energy due to future Daleks visiting. (TV: The Daleks, Genesis of the Daleks, The Magician's Apprentice/The Witch's Familiar, GAME: Lost in Time)
Regeneration-affected
In Victorian London following the Twelfth Doctor's post-regeneration arrival during the dinosaur attack was a focus of energy (TV: Deep Breath) And the Minyan's spaceship; R1C. (TV: Underworld)
The Panopticon on Gallifrey following the Master's attempts to use the Eye of Harmony to enhance his regenerative powers. (TV: The Deadly Assassin)
Bases
At one waypoint within a UNIT base Lab had became charged with vortex energy due to "almost passing through the event horizon of a black hole" (GAME: Lost in Time) when Omega transported it to his anti-matter universe. (TV: The Three Doctors)
Another was the ][Moonbase Laika]] occupied by UNIT on the Moon. (TV: The Moonbase)[additional sources needed]
Snowcap Base in Antarctica (TV: The Tenth Planet) during an Ice Warrior attack. (TV: The Seeds of Death)
Mars during the British Army drilling skirmish. (TV: Empress of Mars)