Originally Posted by
FUBAR007
The rapport was severed when Scott merged with Apocalypse. That's why Jean thought he was dead for so long. Then, Rogue had a vision of him while rescuing Lee Forrester from a hurricane. The vision convinced Jean that Scott was still alive, and she started looking for him. Even after he was separated from Apocalypse, the rapport remained severed. This was confirmed by Scott during a conversation with Logan during "Eve of Destruction".
Based on how Claremont and Lobdell portrayed it, the way the rapport worked was that Scott and Jean could communicate with each other telepathically, and they could sense both each other's presence--even over distances--and condition. On Scott's side, the latter seemed to work like a kind of hyper-intuition. For example, he could use it to find her if she was out of deliberate contact. IIRC, in Legion Quest, that's how the X-Men found Jean when she was unconscious after fighting Legion in the Negev Desert (X-Men vol. 2 #40). The rapport was also a kind of psychic tether linking their minds--it's how Mother Askani was able to pull the two of them into the future to raise Nathan.
Bunn played with the concept, too, with Tyke and Jeen, but their rapport was much less structured and perhaps more intense. They could involuntarily hear each other's private thoughts and sense each other's feelings.