After he got Sheeve'd, they sent him to prison where he was tortured.
The mandos loyal to him broke him out of prison and he regrouped with his Shadow Collective. He was also joined by the Night Brothers.
This was all according to Sheev's plan since he wanted to use Maul to lure out Mother Talzin.
They succeed in luring her out and kill her in front of Maul which breaks him even further. His shadow collective abandons him leaving him with only the mandos loyal to him.
He goes back to Mandalore and begins getting his foothold back there again. Anakin and Obi-Wan are sent in to deal with the Mandaloriean civil war, Ahsoka joins them too, I don't know what the exact details were of them meeting back up, but she did not rejoin the jedi order.
Palpatine gets captured by Grevious forcing Obi-Wan and Anakin to bail on the operation to go deal with Episode III leaving Ahsoka in charge of half the 501st (Rex included).
They fight Maul.
Order 66 comes through, shit gets fucked, Rex saves Ahsoka since he removed his control chip, Maul escapes and becomes a hermit.
I guess the events of Solo happen next followed by the events of Rebels.