When playing Scoop Up Net, do I put all Pokemon stages into my hand or just the Basic or highest stage?
You put all of the Pokemon cards into your hand, including all Stages if applicable.
Source: Rebel Clash FAQ (2020-04-18), TPCi Rules Team (2020-04-30)

Relevant cards

Note: All applicable cards may not be listed below.
SWSH2_165
SWSH2_165
SWSH2_207
SWSH2_207