The first link is from the Goal Tree to the Current Reality Tree (CRT). As long as the Goal is not achieved, the not-achieving Goal stated in the Goal Tree and the not-achieved Critical Success Factors (CSFs), which are Undesirable Effects, are inputs to the Current Reality Tree.
Next is the link between CRT and Evaporating Cloud (EC). A critical root cause from the CRT is very likely to be one of the conflicting entities of an Evaporating Cloud. The Goal Tree may also provide inputs to the EC.
An injection to dissolve the conflict in the EC is an input to the Future Reality Tree (FRT) and the desired outcome are the Goal and CSFs, turned into the FRT’s Desirable Effects, closing the loop and making the Goal Tree the key player of the whole Logical Thinking Process.