Mongo query is taking a while even with index - mongodb

Question

I have been running a mongo test server for a few weeks now and everything has been going good. I had a query to get a count of deleted files and it was running in the sub 1 second range for 140 million documents (44 gb of data). Today, all of the sudden that same query is taking a while. When running explain on the find query it shows it is using the index that is in place but it still takes a long time. The weird thing is, is that this isn't the only query that appears to do this. If I run a query that returns 1 item, it's almost instantaneous. When its returning a set of documents it takes forever (multiple minutes). Below is the query and the explain output from Mongo shell. I've removed the rejected plan to save space, but can put it back if needed. I'm new to mongo so any help is greatly appreciated. I have another query that I've been waiting on for 24 minutes that is just a search on an EventID field which is an indexed field.
db.EventEntries.find({IsDelete:true, TimeCreated:{$gte:ISODate('2017-06-30')}}).explain('executionStats')
{
"queryPlanner" : {
"plannerVersion" : 1,
"namespace" : "Events.EventEntries",
"indexFilterSet" : false,
"parsedQuery" : {
"$and" : [
{
"IsDelete" : {
"$eq" : true
}
},
{
"TimeCreated" : {
"$gte" : ISODate("2017-06-30T00:00:00Z")
}
}
]
},
"winningPlan" : {
"stage" : "FETCH",
"inputStage" : {
"stage" : "IXSCAN",
"keyPattern" : {
"IsDelete" : 1,
"TimeCreated" : 1
},
"indexName" : "IsDelete_1_TimeCreated_1",
"isMultiKey" : true,
"multiKeyPaths" : {
"IsDelete" : [ ],
"TimeCreated" : [
"TimeCreated"
]
},
"isUnique" : false,
"isSparse" : false,
"isPartial" : false,
"indexVersion" : 2,
"direction" : "forward",
"indexBounds" : {
"IsDelete" : [
"[true, true]"
],
"TimeCreated" : [
"[new Date(1498780800000), new Date(9223372036854775807)]"
]
}
}
},
},
"executionStats" : {
"executionSuccess" : true,
"nReturned" : 138570,
"executionTimeMillis" : 177933,
"totalKeysExamined" : 138570,
"totalDocsExamined" : 138570,
"executionStages" : {
"stage" : "FETCH",
"nReturned" : 138570,
"executionTimeMillisEstimate" : 177834,
"works" : 138571,
"advanced" : 138570,
"needTime" : 0,
"needYield" : 0,
"saveState" : 8887,
"restoreState" : 8887,
"isEOF" : 1,
"invalidates" : 0,
"docsExamined" : 138570,
"alreadyHasObj" : 0,
"inputStage" : {
"stage" : "IXSCAN",
"nReturned" : 138570,
"executionTimeMillisEstimate" : 561,
"works" : 138571,
"advanced" : 138570,
"needTime" : 0,
"needYield" : 0,
"saveState" : 8887,
"restoreState" : 8887,
"isEOF" : 1,
"invalidates" : 0,
"keyPattern" : {
"IsDelete" : 1,
"TimeCreated" : 1
},
"indexName" : "IsDelete_1_TimeCreated_1",
"isMultiKey" : true,
"multiKeyPaths" : {
"IsDelete" : [ ],
"TimeCreated" : [
"TimeCreated"
]
},
"isUnique" : false,
"isSparse" : false,
"isPartial" : false,
"indexVersion" : 2,
"direction" : "forward",
"indexBounds" : {
"IsDelete" : [
"[true, true]"
],
"TimeCreated" : [
"[new Date(1498780800000), new Date(9223372036854775807)]"
]
},
"keysExamined" : 138570,
"seeks" : 1,
"dupsTested" : 138570,
"dupsDropped" : 0,
"seenInvalidated" : 0
}
}
},
"serverInfo" : {
"host" : "",
"port" : ,
"version" : "3.4.4",
"gitVersion" : "888390515874a9debd1b6c5d36559ca86b44babd"
},
"ok" : 1
}