As previously noted, the two only have direct contact when Aeris protects Marlene by hiding her with Elmyra. However, there is some implication that the two are connected on some deeper level. In a sense, Marlene inherits some of Aeris, first by becoming a sort of adopted daughter to Elmyra just as Aeris had been, and also through the healer role she attempts to fill during Advent Children. Marlene, in a sense, allows the writers to kill Aeris yet still have a placeholder with a similar expression.

In the game, the biggest connection between Aeris and Marlene is seen during the end video. Going to the window as the Lifestream emerges, Marlene recognizes a familiar spirit: "The flower girl?". This parallels Aeris' mystical innate connection to the Cetra as seen at the Temple of the Ancients.

This spiritual bond is slightly cheapened in Advent Children, where all the children seem to recognize Aeris in some form, rather than just Marlene. However the other children's bond with the flower girl might be explained as either an after-effect of coming to contact with the Lifestream (almost like the opposite of Geostigma), or perhaps might have something to do with the children Aeris' ghost in the Sector Five Church, whereas Marlene's connection has to do with an inheritance (whether it have actually be bequeathed unto her by Aeris, or just a parallel resonance that has no actual bearing outside of extra-textual thematic observation).