the girl that changed his life;
We first meet Ziggy when he is assigned to rescue MOMO from Pleroma. His first reaction to her is that she's merely a child. Then he finds out from Juli that she's not any child, but the 100-series prototype realian. Ziggy found out that MOMO was registered as her daughter. He realizes something is wrong when Juli asks him to bring her to Second Miltia as opposed to returning her to her mother. However, he just sums it up as "strange", and does as he's told.
When he meets MOMO for the first time, they escape to one of the control rooms. She asks him if he's a military Realian, and he responds simply by saying that he's an ex-human, an old relic from the past. After telling her his name, she gives him the nickname, Ziggy because Ziggurat 8 sounds too much like a model number. He immediately has a flashback of when he gave his stepson, Joaquin a cybernetic dog. He didn't give the dog a name, so when he asked he said "Nexus 6". Joaquin responded in the same way as MOMO and named the dog Nex for short. After this point, he slowly, but surely begins to recall bits and pieces of his fragmented memory and the emotions that came along with it.
MOMO not only reminded him of his stepson, but I feel that in many ways, she reminded him of his own situation when he was young. He later finds out that she lost her father, and never had the chance to know him. Furthermore, Juli's actions towards her made him realize that MOMO really didn't have anyone for a parent. At this point, he really begins to treat her like she were his own, even if it's just subconsciously at first.
At the beginning of their stories, Ziggy and MOMO are exact opposites. One is longing to be human, while the other no longer wants to be that way. One of the main themes in Xenosaga is humanity, and all of it's faults, striving to change the future. Little by little, Ziggy realizes this, through not only MOMO, but Shion, Jr, and the others that he found himself traveling along with.
He obviously hates to see MOMO saddened and upset. On a few occasions, he says the wrong thing, and immediately shows guilt for making her feel pain in any way. MOMO's pure spirit and heart draws him to her. He feels comfortable around her, unlike anyone else.
When MOMO is kidnapped, he wanted to go alone to rescue her. He didn't want anyone else to take on the burden. But after a lot of persuasion, they all went together. Although during the scene where MOMO is rescued, we don't see a whole lot of Ziggy, one can certainly infer that he's going through a roller-coaster of emotions. Not only the initial relief knowing that she's all right, but then finding out that she had no memory of who she was. Perhaps at that moment he may have felt saddened, knowing that everything they had been through together up until that point was forgotten. Though thankfully, it wasn't MOMO, but a Kirshwasser. When they finally find MOMO, I'm sure that Ziggy was filled with anger at Albedo for causing her pain.
The bond deepens
In Episode II, Ziggy goes even further to play the father role for MOMO. Not only does he protect her while escaping from Richard and Hermann, but he tries to be supportive and positive when her mother isn't. He then asks Juli if she could try to think of MOMO as another child, instead of a replacement of the one she lost. Perhaps at some point, Ziggy was feeling this way as well, but then realized that he should try to change the way he thought of their relationship. At any rate, Ziggy clearly wanted to give MOMO what he had lost, two parents.
Then, during MOMO's analysis, he stays by her side to comfort her. When she realizes that her heart isn't real-- an optional function, she reaches out to Ziggy, upset and scared. He reaches back to her, but then, her personality is turned off. Ziggy clearly looks upset and saddened to see her that way.
When MOMO was hacked by Albedo, Ziggy pleads with Juli not to push the button to end her life. The last thing he wanted was to have another child taken from him. However, even though she didn't push it, MOMO cut her neural pathways in order to save the Y-Data. Ziggy and Juli rush to her side. When Ziggy sees MOMO lying there on the floor while Juli tries to resuscitate her, he remembers loosing Joaquin to Voyager.
In MOMO's subconscious domain, he he learns more about Sakura. He pushes everyone forward, wanting to do everything he can to save her. I think that although the Y-Data was lost in the end, Ziggy was relieved that MOMO was all right, along with everyone else. Though we really don't know what happened between MOMO and Ziggy after the dive, I'm sure both Ziggy and Jr were there to support her after loosing the Y-Data. When Shion is reunited with the party on the Elsa, MOMO and Ziggy are standing next to each-other in a conversation. I thought that was adorable.
At the end of Episode II, MOMO runs to Ziggy's side after his attack on Voyager backfired on him. Then, she pleaded with him not to move when he got up to punch a hole in the wall. After that, he fell on the ground, and again MOMO was there for him. Afterwards, she spends a long time trying to repair him back to normal.
Daddy's little girl
We aren't given any details about what happened in between Episodes II and III from Ziggy and MOMO's perspective. However, since Juli was busy working with the S.O.C.E. and Shion during the Gnosis Terrorism, I'm fairly certain that MOMO went to stay with Ziggy and Jr. on the Durandal.
During the first part of the game, we really don't see much of them. This is mainly because of the game focusing on Shion, KOS-MOS and T-elos. In fact, Ziggy and MOMO's interactions are barely there through the bulk of the last Episode. However, he's always nearby, ready to help her if she needs it. Although she's right there when Ziggy encounters his past, and all of his memories return, they really don't have any interaction. Just before fighting Zarathustra, Ziggy is seen kneeling next to MOMO helping her stand.
Although, one of the most significant (and amusing) tell-tale sign about the relationship shared between Ziggy and MOMO is not in the actual story. However, it's one of her tech attacks! MOMO can learn Ziggy's Sword Fish attack. Instead of fighting with a bow, she runs up and pounds the enemy just like Ziggy! It also does a great deal of damage. How little MOMO can do more damage than Ziggy on some enemies is beyond me. But even so, I bet Ziggy is proud of that!
The journey's end
At the very end of the story, Ziggy stays on board the Dammerung with Juli and MOMO. He promises Jr that he'll do everything he can to protect and take care of them. Whether or not they end up living together is uncertain. Although I'm sure that if they aren't right at the end, they will eventually. MOMO wants nothing more than to be with Ziggy and Juli, the two people she loves the most. I'm sure that this is what Ziggy would want the most as well.
By the end of the series, Ziggy has come full circle, thanks to MOMO for the most part. He no longer wants to erase his memories, but he wants to keep them with him. Instead of being an emotionless machine, he realizes that he's still a human being, full of emotion. He's also learned to accept his many faults. On the other hand, MOMO has received her wish as well. She's the closest to a human being as an artificially created human can be.
Although the database says that no one knows how long Ziggy's brain will stay alive, I'd like to believe that Ziggy will be there for many more years. Since MOMO is a transgenic realian, he'll want to stay around to watch MOMO grow up, and maybe one day have a child. This was something that he never had the chance to do before.