What was going on with Tom Hagen?

Tom, being adopted and of Irish descent, was never allowed to be a "made" member. Very similar to Henry Hill in Goodfella's. This always made Tom feel distant from Michael and Sonny. He knew he could never be a true, full member of the family.

As Napoleon pointed out, by this time Michael was becomming paranoid of everyone. Tom was more interested in keeping peace, and to some degree he twisted some facts to get Michael to back down on his personal vengeance spree. That whole thing about leaving Roth alone was more about keeping the family out of a war than anything else. Tom was more practical that way.

Ok, I'll give it a first try, but this may not be too complete (and I haven't seen it for quite some time).

In fact Tom's role in the family has always been a bit difficult. While he is to some degree a member of the family (and not just the "family", but the real Corleone family core) and has always been a valuable member, he on the other hand has never been a complete member and thus there was always a bit of a border (be it only a small one), which didn't allow him to take any more responsibilities in the business than those of the Consigliere (which is still an important role, of course). And I think especially between Michael and Tom there has been a little bit of a distance, at least a larger one than between Tom and any of the other brothers, even if Michael probably valued and respected Tom very high, of course. This is adressed in some dialogue in the movie (or maybe the first part?), I think, when Tom says to Michael that he has always felt a bit of a distance from him.

Another aspect is that this dialogue ocurs very late in the movie, I think, and Michael was becoming increasingly paranoid and defensive (which is also evident from this dialogue itself, when he wants to go after Roth for any price), and probably felt abandoned or betrayed by many important people in his life, be it Fredo or Kay. He maybe also remembered the dialogue earlier in the story when Tom asked if he could take a higher position in the business, but was denied (if I remember correctly). So I think he was suspecting Tom to forsake him, too and to cut the connections to the family and the business in order to strive for higher personal success. But in fact Tom has always been one of the most loyal members of the family (maybe even motivated by the fact that he never felt 100% accepted, especially by Michael) and is thus hurt when Michael forgets this.

The answer is at the very end of Godfather Part II...the flashback scene. "You discussed MY future"...his pop and Sonny doing it was one thing but Tom getting involved was a bit too much for Michael. And Michael never forgets.

This scene is an example of the overreach Michael was doing throughout the film. In the first Godfather, the idea of killing all the heads of the Five Families seemed outlandish - but it worked, because all of them were lulled into thinking that Michael was either weak and/or didn't want to fight them anymore. In Part II, the main enemy Michael had left was Roth, who was no dummy. He knew that Michael was responsible for killing the heads of the Five Families, and he probably had some idea that Michael eventually would figure out he was the one who wanted him dead by using Fredo. Michael decides that he wants to have Roth killed, even though there wouldn't be any beneficial reason to do so - Roth, after all, was trying to run to Israel to escape from Michael; Roth was also not a healthy man and although he wasn't dead yet it would only be a matter of time before God did what Michael wanted to do. But Michael, being a proud man, wanted to have Roth dead for the attempt on his life (it was this same pride that caused him to allow Fredo be executed after their mother's death, even though there was no other reason to have him killed).

Tom, who was acting as Michael's right-hand man, was correctly trying to talk Michael out of an action that could have come back to bite him in the ass (if Roth's assassin had been wounded instead of killed in the attempt, bet your ass he makes a deal to finger Michael as the person who gave the order - and that guy probably wouldn't have had a brother in Italy Michael could have flown in to intimidate him into reversing himself). Michael, though, was too far along in his hatred to listen to reason. For that reason, he was willing to kick Tom - whom he considered as a brother, despite not being a made man - to the curb unless he went along with his plans.

I think Michael wanted Tom to leave and had other entities come forward with job offers to Tom.

He (Michael) told Tom what he wanted to hear the night of the shooting on the estate;"You'r my brother" to get Tom on board until he returned from Havana.

No No No you have it all wrong. The simple answer here is that Michael pushed Tom to the rear because he was plotting his revenge and the wrap on Tom was, although he was a trusted member of the family, he just wasn't a strong "War Time" Consigliere. This thought was first brought up when Sonny wanted to go to the mat after Vito was shot and Tom wanted to make deals calling the whole mess "business". Knowing how Sonny felt about Tom, remember while Tom wanted to make the deal it was Michael who came up with the plan to kill Virgil Sollozzo. Michael was sure not to make the same mistake that Sonny did. Once Michael took over he used his father as his first "Consigliere" saying that there would be no better adviser than his own Dad. That decision prove valuable as it was Vito that sniffed out the entire plot against Michael even telling him that the person who comes to him with the deal is the snitch. Michael had plans on wiping his enemies out and didn't want Tom talking peace around him, which he tried to do right before Michael tells him he can take his entire family and go to Vegas. The question of staying was offered in Italian, which was serious business. To agree to stay is to agree that this was going down Michael's way and there would be no talk of peace. He does use Tom to deliver the message or rather choice of death to Pentangeli (aka Frankie Five Fingers). The next to last scene flashback shows that it wasn't the first time Michael put Tom in his place.

This may be a conspiricist theory to some maybe most but im not necessarily one i just watch good shows or movies that intrigue me over and over to catch little clues that people who watch once overlook and see just the overall story unfold. Directors and writers are very smart, maybe out there, so to me there is more that meets the eye. The last scene in the Godfather part two is when Michael tells them he's enlisted in the army which everyone is unhappy with and it is at his father's birthday party. Perhaps everyone is upset with him and this has a reasoning in the entire part one and part two movies. Michael always seems to downgrade Tom towards the end of part one and the entire part two which seems to make Tom ask why and get angry. Tom has always been said to be off the streets so maybe I believe Tom could've been the culprit in the whole backstory of these movies. An example is when Michael visits Hyman Roth and his home in Miami Roth is watching the football game between the USC Trojans and the Notre Dame fighting Irish. Trojans are Roman in Italy versus the Irish which Tom is Irish, Italian versus Irish.

I think it goes way back to Italy when young Vito (Robert DiNiro) constantly shows his favoritism for Michael over the other children; of course he loved them all, but how many times did he show this special feeling toward Michael in words and actions? Perhaps it was because he was the youngest, but whatever the reason, it was all too evident thruout all 3 movies, and this special feeling for Michael is what made him turn into the Don he became, to live up to his father's expectations.

*I think Michael wanted Tom gone and got him all the jobs he had turned down plus he (Michael) knew he could manipulate Tom by telling he was respected and a" real brother" as he did the night at the assassination attempt.

Tom wanted to belong and would do anything for it including being loyal and telling Frankie Five Angels to open up his veins and kill himself for going against the family.

Or Tom could take his wife, his kids and his mistress and move to Vegas!