This article contains major spoilers for the game.
The R-Gate is a time-travel gate that can be opened or closed by inserting the Key of Time in the chest of a R-Series robot and turning it. According to Valghis, it only works with him and Rodea, the Key of Time having refused the others.
The R-Gate is opened twice in the game.
The first time happens after Rodea stops all the Chronos Towers. Valghis shows up, reconstitutes the Key of Time and uses it on Rodea to open a R-Gate that leads 1000 years in the past. This gate is crossed by Valghis, Rodea, and Ion (aboard the Ion Wave).
Later, after Geardo is permanently defeated, Rodea opens another R-Gate (using the Key of Time on himself) to let Ion (with the Ion Wave) go back to her era (1000 years in the future) while he stays behind to close the gate. Ion ends up in a new future.