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Below is a script that can get a SharePoint online root site and subsites. How do I get 2 , 3 and 4th level of subsites? For example:

Generate ClientContext function so we can reuse

function GetClientContext($SiteCollectionUrl, $username, $password) 
{
     $securePassword = ConvertTo-SecureString $password -AsPlainText -Force
     $context = New-Object Microsoft.SharePoint.Client.ClientContext($SiteCollectionUrl) 
     $credentials = New-Object Microsoft.SharePoint.Client.SharePointOnlineCredentials($username, $securePassword) 
     $context.Credentials = $credentials
     return $context
}

Function to loop through subsites

function catchsubsites ($subsiteurl)
{
    $clientContext = GetClientContext $subsiteurl $username $password
    $rootWeb = $clientContext.Web
    $childWebs = $rootWeb.Webs
    $clientContext.Load($rootWeb)
    $clientContext.Load($childWebs)
    $clientContext.ExecuteQuery()
    #do something on top level site
    write-host $rootWeb.url -ForegroundColor Yellow
    foreach ($childWeb in $childWebs)
    {
        #do something for each subsite
        write-host $childWeb.url -ForegroundColor Yellow
        #see if there are any subsites beneath this and loop all of them too
        #catchsubsites $childWeb.url
    }
}

Finally run the function to get it all started!

catchsubsites $SiteCollectionUrl

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In your foreach loop, you commented out the line #catchsubsites $childWeb.url. That's the recursive call you need so that you can travel throughout the tree of sites in your collection.

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There is generally no need to create ClientContext multiple times. I have tested equivalent code in c# and it worked fine without duplicates (in your current solution if you uncomment recursive call you will have duplicated entries) and with single ClientContext:

function GetSubsitesRecursively($clientContext, $web){
 $subsites = $web.Webs;
 $clientContext.Load($subsites)
 $clientContext.ExecuteQuery()
 foreach($subsite in $subsites)
 {
    write-host $subsite.Url -ForegroundColor Yellow
    GetSubsitesRecursively $clientContext $subsite 
 }
}

function GetSitesTree($rootSiteUrl){
 $clientContext = GetClientContext $rootSiteUrl $username $password
 $rootSite = $clientContext.Web
 $clientContext.Load($rootSite)
 $clientContext.ExecuteQuery()

 write-host $rootSite.Url -ForegroundColor Yellow
 GetSubsitesRecursively $clientContext $rootSite
}

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